you'll have a 3.06 1st gear with the 700R4, as opposed to the TH350s 2.52. the advantage there goes to the 700R4. that coupled with the overdriven top gear, the 700R4 is in a clear advantage, providing it is in good condition. flush out all of the old fluid, put in a fresh filter and gasket, and make sure your TV cable is adjusted properly (VERY critical). also install a large trans cooler when you install it. if your rig sees mud often, make sure its located somewhere where mud wont get to it to clog it up, and make sure it gets adequate air flow to cool the trans. doing these things, and being sure to keep it out of OD when playing, you shouldnt have a problem with the trans, despite their shady reputation. most failures are due to gears in the rear being too high (most were coupled with 2.73 or 3.08 gears) and oversized tires, putting more stress on the trans. with your 4.10s and an actual 36" tire, you should pull around 1750 @ 65 mph, so you should be fine there.
as for the transfer cases, both being chain driven cases, i'm going to say they are going to be close internally as far as strength. the 208 has the advantage of a lower low range. 2.62:1 vs the 2:1 of the NP203. up until this point, the 208 has the advantage. both being chain driven cases, i'm going to say they are going to be close internally as far as strength. the 208 has the advantage of a lower low range. but, being that the case of the 208 is aluminum in is more prone to damage offroad than a 203 would be. on the up side the 208 is lighter, more compact, and is clockable (DIY4X makes a reasonably priced clocking ring, so you can clock it up to get it a little more out of harm's way.). the 203 should be a fixed yoke, where the 208 is a slip yoke with no option of an SYE. i'd say with a 208 and a decent skidplate under it, you cant lose with the 700R4/208.