what did you do for brakes, I'm assuming you used some form of a hydroboost system

Factory vacuum brake booster. The engine has a very powerful cam driven vacuum pump.

if I choose to use the aw4 trans, you mentioned needing a higher stall for the Mercedes diesel. would any of you in here happen to know the factory stall speed or where I can find a higher stall torque converter

I'm not sure you can get a different stall for the AW4, I had talked to a local shop about it when I did my swap. The stock converter turned out just fine behind the diesel (Kubota not Mercedes) but I also had a stock converter with a 700r4 and Mercedes, so I think you'll be fine.

ok then my next question I looked up the radesigns trans controller but the aw4 will no longer shift automatically. Has someone else come up with a better controller for it or am I better off using a 700r4, bein as I'm gunna daily drive my jeep and I don't wanna have to be shifting It the whole time

Having run both a factory 700r4 torque converter (1600rpm behind my setup) and one with higher stall (2200rpm, advertised at 2400rpm) I can say the higher stall is much better in all aspects except for milage. I now have 35" tires on the jeep and the higher stall proves even better, seems to be stalling at about 1800-2000rpm now.
Keep in mind in 1985' Mercedes increased the stall speed on this engine's transmission to 2600rpm for good reason.

I have no knowledge of doing this with the aw4, but search around as I remember it being done around this forum recently. The aw4 is a good transmission. 700r4 is 100% mechanical but requires some extra work. IF you can get the aw4 to shift correctly I'd venture that route, especially since you already have what you need to experiment (nothing to lose). It would be super easy and clean, not to mention cheaper.

I will agree with that since I'm on a somewhat limited budget lol... What kinda mileage are you getting with the bigger ip an turbo?. I haven't been able to find a definitive answer for the aw4s stall speed I will keep reading into a stand alone controller but I also have a 700r4 sitting in my shop as well so I may end up following the route you've made.... Did you ever figure out you're over heating issue

You don't need to buy a stand alone controller for the AW4, if it's an early (pre 98 I think) Jeep it already has it's own separate controller for the trans. You just need to keep the TPS and the TV cable as well as the RPM signal from the flywheel. I believe you'll get better MPG's with the AW4 because it locks up in 3rd and OD.

I'm srry I guess I shoulda said mines a 2000, I was readin up on that last night though about how to make it still work. Would you guys have any suggestion on how to make the tps work on the Mercedes, ive got a few ides I'm jus curious if anyones tried it yet