Fratt -
Your only choice here is going to be to buy the AA kit to adapt the Dana 18 transfer case to the TH400. I've been through this and believe me, I researched every angle. Many people will led you to believe that a Dana 18 will bolt right up behind a TH400 that originally had a Dana 20 (early 70's Wagoneers), but that's not true because that setup uses a very funky output-shaft/gear combo that would HAVE to be the factory stuff and is therefore available only in 26-tooth for the Dana 20. It would be possible to build a Dana 18 with the Dana 20 2.03 gearset and use the factory stuff, but let's face it, that sucks...
Once I figured this out, I determined that rather than spend $500 on the AA unit, AND (this is big) have a professional shop install the new mainshaft in the auto trans, I'd spend the money on a T-18 4-speed and use IH Scout parts to matre the whole mess up and use the Dana 18 transfer case and keep my offset rear.
I did this 3 years ago and never looked back. The swap from auto to stick is alot of work, but it's all labor - there's no rocket science here, and the parts you need are readily available in the junkyards from stock applications.
That's what I recommend to EVERYONE with a Q-trac. This could start a war, but I love the Dana 18, think the AMC 20 can be fine with a little beefing, and think an auto can't hold a candle to a stick off-road -especially when you consider the kick-starting, no need for a trans cooler, lower gearing (even with the torque converter mulitiplication an auto isn't close), more gears (3 vs. 4) and best of all, the compression braking.
PLUS - you can sell your Q-trac low-range unit for $100 and maybe even get some money out of the trans! Good Luck!
Chuck Hadley