Hi Thomas,
The th400 has a 32 spline output shaft whereas the th350, 200r4, and 700r4 all have 27 splines.... so you'll have to change the transmission end of your driveshaft no matter which one you choose.
The 200r4, which is the one I went with, is pretty much a bolt in, excepting for moving the cross member back. (350 cid/th350) and trimming the balance weight at the transmission end.
The th400 cross member is different and the transmission is a couple inches longer, so you will have to find/build a new driveshaft. I've also read that there's minor clearance issues using the th400.
Personally, I like the 200r4 for the wider gear ratios (0.67 to 1 overdrive and 2.67 to 1 first gear) for highway driving. But if you choose the 200r4, make sure you get it rebuilt with heavy duty internals..... 400 hp is a lot for the original "off the shelf" units where as the th400 could take that kind of hp.
As for the rear gears, 3.55 should make a nice street/highway combination.... Montelishi originally had 2.73's, which are really nice on the open road, but a little lagging at the stoplight. I eventually went to the 3.42's. Still a little slow at the light, but I've pulled around 20 mpg on the highway with them.
There are a few threads here that discuss who likes which better, I'm sure more will weigh in eventually.
Good Luck with your swap,
Scott.