The loss of acceleration is less than you might think. Really, the final drive ratio only matters up to 25 mph or so (when you shift out of 1st gear) and again near top speed. But you will, I think, definitely notice the difference when taking off from a stop. With the 3.45 gears, you'll have 16% less torque (and hence acceleration) at the rear wheels.
I'm actually somewhat in the middle of the same odyssey. When my current TR3 came to me, it had 4.1 gears and no OD. I first installed an overdrive, then later went to 3.7 gears when the 4.10 axle broke. Now one of my "back burner" projects is replacing the 4.1 gears with 3.45 (the 3.7 gears are in a different axle that I had on hand).
Unfortunately, changing the gears can be a lot of work. Without the special tool for setting the pinion depth, it becomes a trial and error process to find the right depth. It is adjusted with shims, so each time you check the pattern, then remove the pinion & bearings to add or subtract shims, put it back together and try again. There is a trick that helps (grind down the inside and outside diameters of the old races, so they will slip easily in and out of position) but there is still a lot of "rowing" in and out. Then once you find the pinion depth, repeat the same process with the shim pack that sets the pinion preload. Hopefully you'll get lucky and can keep the same shim packs for the carrier bearings (since you'll be using the same carrier), but you'll have to double-check and adjust those if necessary. The final proof is when you can see that the contact patch is centered on the gear teeth.
There are a few more photos of my Stag diff (not identical, but the internals are very similar to the TR diff) at
https://s258.photobucket.com/user/TR3driver/library/Stag diff Along the way, you can see some of the special tools I made up, mostly just lengths of cheap hot rolled steel drilled and shaped to suit. The gear puller is a HF special, modified for extra reach with some coupling nuts & bolts from Home Depot. I got the micrometer and dial indicator from Enco
https://www.use-enco.com/CGI/INSRHM as I don't really trust the precision of tools from HF. (Honestly, Enco may not be any better, but I think they are.) They frequently have a 1" dial indicator & magnetic base set on sale for under $25, but I don't see it at the moment.