Ditto, Spaghetti Legs' questions. Any differences can influence fit and comfort.

Is the frame geometry identical?

Identical saddles, handlebars, brake levers/hoods, crank lengths, gearing, bar wrap, etc.?

I have two road bikes, an '89 Centurion Ironman steel bike, and a '93 Trek 5900, then Trek's flagship carbon fiber bike and still a very good bike by any standards. Both diamond frames, since Trek hadn't yet jumped on the compact frame with sloping top tube popularized later by Giant.

But it's taken months to get the Trek fitting as well as the Ironman. There were many small differences so I took a methodical approach, changing one thing at a time. I have an old C1-C2 neck injury, so fit is critical.

• The Ironman is a 57 or 58cm frame; the Trek, 56cm. Both fit me fine, but that's enough difference to affect reach, etc.
• The Ironman had a Selle Italia SLS Kit Carbonio, which I liked so well I swapped it over to the Trek. But it took months to find a suitable replacement for the Ironman, which now wears an excellent Bontrager Ajna cutout saddle. Without identical saddles it took a lot of trial and error adjustments to suit me.
• A year ago I switched the Ironman from the original 125mm stem to a 90mm. Huge difference in comfort. Recently I switched the Trek from the original 140mm to a 90mm and more contemporary stem -- similar weight, but fatter tube and more rigid.
• The Ironman's original classic drops have always been fine. I tried three sets of drops on the Trek before recently finding an FSA Omega compact that was a huge improvement.
• I'd already moved the aero brakes/hoods on the Ironman up higher, closer to the 1950s-early '60s style, and adjusted the brake lever angle to be vertical rather than splayed outward. Much better. But that didn't help much with the Trek because the original stem and handlebars were different from the Ironman.
• Switching to brifters with elongated reach on the Trek just made the fit worse. Too stretched out. It's only a few centimeters but felt miserable. Switching to a shorter stem and compact drops was a huge improvement.
• The Ironman has a single wrap of foam "cork" bar tape; the Trek has Arundel Synth Gecko, very thick rubbery stuff, and it's double wrapped over some generic foam tape. Some difference in feel on rough roads over long rides.
• The Ironman has 172.5 crank arms, the Trek has 170.
• Seat tube angles are slightly different. Top tube lengths are different.
• The Ironman had a 50/39 double chainring set (now 50/38) and 13-25 freewheel (now 13-28); the Trek has gone through several gearing changes before I returned to the Biopace 52/42 double and 14-28 freewheel it started with back in April.
• Wheelsets were nearly identical (not much difference between Araya CTL-370 and Wolber Super Alpine rims), but tires were different. I had 700x25 on the Ironman, and identical model tires in 700x23 on the Trek. Made a difference in overall feel. I recently switched the Trek to 700x25 and now it feels much better on chipseal and rough pavement.

Regarding gearing, I wouldn't say it makes much difference which combination of chainrings and rear cogs. As long as it has a decent range for my terrain, no big deal. And the Biopace sorta-oblongish-ovalish chainrings feel a little different but not a huge difference -- mostly I notice some advantage on climbs at a lower cadence.

But what really mattered was the gear steps. It's annoying when I'm too aware of the gearing steps, so I went through a lot of changes in chainring and freewheel combos to find a seamless shifting setup for both bikes, without jarring steps between cogs. That alone can save some muscle stress on long and/or fast rides on hilly terrain, with lots of shifting and cadence changes.

I think I've finally got both bikes set up to feel equally comfortable. But it took a lot of tinkering.