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 Merle arrived to find the "Forest City" obsessed by the pursuit of genial desperado Blinky Morgan, who was being sought for allegedly murdering a police detective while trying to rescue a member of his gang who'd been picked up on a fur-robbery charge.

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"Forest City"
Cleveland's nickname based on an Alex de Tocqueville description in Democracy in America from 1835. Like Blake's America a Prophecy, we have another text written concerning the state of America and democracy, observations of the New World's grand experiment. I read only a little on Tocqueville so my instant judgment of him as "the early 19th Century Ayn Rand" probably doesn't hold a lot of water.

"genial desperado"
The friendly criminal.

"Blinky Morgan"
The leader of a gang of fur thieves, summarized by Pynchon in the rest of the sentence. The dates of the Blinky Morgan fur robbery on January 26th, 1887 to the capture of Blinky on June 28th, 1887, overlap the dates of the Michelson-Morley Experiment (April to July, 1887). The town was obsessed with his pursuit because there was a reward of $16,000 for Blinky and his gang's capture. Also maybe because he killed a detective but people probably hated detectives properly back then.

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 So despite days and nights of traveling, Merle had an eerie sense of not having left Connecticut—same plain gable-front houses, white Congregational church steeples, even stone fences—more Connecticut, just shifted west, was all.

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Even though the Connecticut land ceded to Pennsylvania had happened about one hundred years ago, the Connecticut settlers who had not been killed in the Pennamite-Yankee Wars were granted Pennsylvania citizenship and allowed to keep their lands. Which means Northern Pennsylvania has its roots in Connecticut culture.

"So despite days and nights of traveling"
Movement without movement. Like the vortex Heino Vanderjuice mentions earlier. Or like a pinwheel where movement and stasis are somehow combined. Lack of change means lack of movement, lack of advancement. What does this mean for Merle?

"an eerie sense"
This feels a bit paranormal, something akin to the opposite of unheimlich (un-unheimlich?), where Merle is feeling a sense of home but in a strange place (not heimlich because it is eerie and, so, un-unheimlich!). It's as if, as a person from Connecticut, the frontier does not exist for Merle because it's Connecticut all the way down.

"just shifted west"
Perhaps a reference to light and how it retains the same speed (or, in the analogy, the same architecture of Connecticut) but shifts from red to blue or blue to red depending on the viewer's relationship to the light's movement. This land looks like Connecticut but shifted west, or viewed from the future (Merle) looking into the past (or is it the opposite being that the land Merle has arrived in is newer than the land he came from?). Being that light is our major theme at the moment, the usage of "shifted" has to be referencing the properties of light, especially since this shift is based on what Merle is seeing around him. He's moving west, toward the future, but looking into the east, the past. I guess that's kind of a property of light too! That whatever we see is already past due to how long it takes light to hit our optical organs.

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 This strip of Ohio due west of Connecticut had for years, since before American independence, been considered part of Connecticut's original land grant.

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I think this strip specifically might be what is known as the Western Reserve and possibly the strip through Pennsylvania was just known as "Settle Here at Your Own Risk"? Or maybe it's just because the land was given to Pennsylvania as America was being established and the Ohio portion was simply more Connecticut until the state ceded the land to the United States as part of the Northwest Territory in 1800. But not before Moses Cleaveland founded the worst city in the United States!
    Anyway, the university where Merle is headed was called the Case Western Reserve University except that Pynchon refers to it as the Case Institute, something it wouldn't be called for decades. Which is weird because calling it by its original name fits in so much better with Merle's story!

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 Merle had been born and raised in northwest Connecticut, a region of clockmakers, gunsmiths, and inspired thinkers, so his trip out to the Western Reserve was just a personal expression of Yankee migration generally.

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"northwest Connecticut"
The county of Litchfield, or possibly Hartford. Having grown up as a Bay Area resident in California, I know that looking at a map and describing the area of the state I grew up in as "Northern California" can seem to be at odds, so I won't judge if the people of Connecticut want to call Hartford County "northwest Connecticut."

"a region of clockmakers, gunsmiths, and inspired thinkers"
Seeing as how gunsmith is included here and assuming Pynchon means Samuel Colt who was from Hartford, it strengthens the argument for northwest Connecticut being Hartford County. Not to mention how every mention of Merle in Connecticut has been in relation to Hartford and Yale. Oliver Winchester was also from Connecticut but New Haven County rather than Hartford and New Haven is decidedly southern Connecticut.
    Eli Terry is probably the clockmaker, also from Hartford County although he later moved to Northbury (later Plymouth) in Litchfield County so maybe I'll just believe northwest Connecticut applies to both counties. Apparently his work ignited the industrial revolution so that's probably important.
    I don't know who the inspired thinkers might be since there are too many people who could fall under that category. J.P. Morgan is from Hartford so we'll just go with him as the best example since he'll probably be important later.

"Western Reserve"
The original charter for Connecticut from 1662 marked its western border as the "South Sea" (Pacific Ocean). So Connecticut was a long-ass state. Almost immediately there were conflicts with New York which were ultimately resolved so that the long stretch of land to the Pacific was cut off from the rest of Connecticut by New York's dangly bit. The portion of Connecticut west of New York was called the Western Reserve. Unluckily, Pennsylvania also had claims to this land via the Dutch and also because it was sold to them by the Iroquois which seems like a reasonable trick to play on the European invaders.

"personal expression of Yankee migration generally"
Merle is headed toward Cleveland, Ohio, which would have one time been a part of Connecticut according to the original charter and the Western Reserve. So Merle's trip can be seen as merely an example of another Connecticut Yankee heading out to settle Connecticut's western frontier. He refers to himself as "Yankee" to remind the reader of the Pennamite-Yankee War fought between the people of Pennsylvania and the people of Connecticut over this chunk of land. I use the verb "remind" so it seems like I once knew about this interstate war but had forgotten about it. And maybe that's true and I didn't just learn about it this late in life because how am I supposed to remember what I have forgotten?

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 "Mr. Rideout, we wander at the present moment through a sort of vorticalist twilight, holding up the lantern of the Maxwell Field Equations and squinting to find our way. Michelson's done this experiment before, in Berlin, but never so carefully. This new one could be the giant arc-lamp we need to light our way into the coming century. I don't know the man personally, but I'll write you a letter of introduction anyway, it can't hurt."

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"Mr. Rideout"
That'd be Merle! He's the guy with whom Heino is speaking! Try to keep up!

"wander at the present moment"
To wander: "walk or move in a leisurely, casual, or aimless way." Vanderjuice surely means to invoke the aimless choice in that definition due to science's current lack of knowledge about Æther (what is known at "the present moment").
    "The present moment" can be seen as a boundary or a dividing line between the past and the future. It contains all movement, all discovery. Pynchon sees this particular present moment (the end of the 19th Century and, probably the beginning of the 20th Century, judging by the size of the book!) as a critical juncture between many old academic ideas and what they will be replaced by. Or, perhaps, what new ideas will be killed by those who have gotten rich off the old ideas.

"a sort of vorticalist twilight"
The darkness of a deadly storm (vortex/tornado/hurricane) with a hint of danger due to the high winds and debris of cast aside or outdated theories. That's probably what he means! "Look out! Hollow Earth theory coming right at your head!"

"the lantern of the Maxwell Field Equations"
Published in 1861 and 1862, they proposed that light was an electromagnetic phenomenon, unifying theories on light, magnetism, electricity, and electromagnetic radiation, which had all been described previously as separate phenomena. Anyway, that's the simple gist of the Wikipedia entry and even that summation is threatening to crack open my brain. I suppose I should understand how light works much better than I currently do, seeing as how this book (at least this first section), is really focusing on the light theme.
    This phrasing is clever because the lantern is what is needed to make our way through the darkness and the lantern uses light and the Maxwell Field Equations provide answers to how light works to help us see our way to understanding light. And electricity. And, um, magnetism. Reading the rest of the Maxwell Equations Wiki entry has provided little help except to remind me how dumb I am.

"Michelson's done this experiment before, in Berlin, but never so carefully"
The problem with Michelson's previous experiment was that his device was subject to experimental errors too large to provide any meaningful results.

"This new one could be the giant arc-lamp we need to light our way into the coming century"
Fitting words as this experiment will, more or less, destroy science's fascination with Æther, allowing it to move forward in different directions, and eventually leading to Einstein's theory of relativity. Also fitting because he compares it to a giant arc-lamp needed to light the way. Again, he uses the metaphor of light to describe our ever-increasing knowledge of light itself. Also knowledge is always said to illuminate. I can't do all the math needed to understand how magnets create electricity which produce light (or whatever is going on there!), so instead I just look for dumb metaphors and apt analogies! I haven't taken a calculus class in 30 years but I've re-read like twelve Xanth novels in the last few years so that probably explains my intelligence level.

"it can't hurt"
When somebody says, "To tell the truth" or "To be honest," they've either just previously lied to you or are about to lie to you. In the same vain (vane? vein?), when somebody says, "It can't hurt," you better believe it fucking will.

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 "Think this is worth going out to Cleveland for?"

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Is anything worth going out to Cleveland for?

I'd suggest the use of Cleveland might be some clue to something Pynchon is saying, like how boundaries "cleave" the "land." But, historically, that's just where the experiment took place.

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 Indeed one finds in the devout Ætherist a propensity of character ever toward the continuous as against the discrete. Not to mention a vast patience with all those tiny whirlpools the theory has come to require."

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Damn. This whole "continuous versus discrete" thing is probably really important to the bigger picture! This sounds like he's talking about something more than just dissecting light and electromagnetic waves and an imaginary substance filling up our nostrils and buttholes. Since Vanderjuice's monologue (which ends with these two lines) is about the faith often needed to believe in Æther, I should just view this as an analogy of religion. Even though Ætherist looks like Atheist, the Ætherist would be the stand-in for a true believer. Their view is toward the infinite and the continuous, the undying soul that continues on in both directions from the finite body it only momentarily possesses. While the Atheist exists in our discrete and finite mortality, the only life we have to live. The Atheist's view is also the more scientific view, being that perception of evidence is only possible with our consciousness which only exists while we're alive.

"a vast patience with all those tiny whirlpools the theory has come to require"
While this can describe a scientific theory, it's a poor theory which scientists would probably only use because it was somehow working for some instance but knowing something better and which made more sense without needing a ton of exceptions would come along. So, really, the tiny whirlpools would be religious dogma needed to explain The Bible better, or to handwave away obvious contradictions.