There are NT upgrades the same at the WT axles, but I'd seriously recommend finding a good set of WT axles (that have already been re-geared to 4.10 or so) and swap those in. The gearing will be right for the 33-35" tires.
Trussing and welding the AMC20 will make it plenty strong for those size tires, actually stronger than a Dana44.
As far as Re-gearing also goes...if you are going to put in Tru-Tracs front and rear you'll have to re-set backlash, etc anyway so you might as well (Aggghhh The dreaded MAW's!) re-gear then while everything is out.
Do you run a 4 or 5 speed transmission and will you use it on the highway? this will help determine the best gearing.
TrueTrac's are pretty solid and will do well in most offroading situations.
Front Tube fenders...tons of people make them and they are all great products for the most part I like Kings OffRoad's Products - KORE, King's Off Road, King's Off Road Enterprise, Off Road Chassis Turn-Key Buggies
That link is for the YJ fenders but he always has CJ tube fenders in stock (website just hasnt been updated in a while)
the TJ flares, tube fenders, and body trimming should give you plenty of clearance for 35's if you go to a 4.5" Lift...I dont think 2.5 is going to be enough personally unless you wont be putting it in any flexy situations.
If its going to be getting a lot of city/highway use I'd also consider going to 4 wheel disc breaks. Lots of great DIY writeups out there and complete setups as well depending on how much you want to spend. But power 4wheeldisc brakes will make it MUCH safer to drive than manual drums...
1985 CJ7 Project
Phase One :
5.3L Vortec/4L60E, Moser axles for AMC20, Twin Stick'd Dana300 - Completed
Bedliner, Rollcage, Seats, BESRK Rear Bumper w/ tire swing, Soft Top, and a few other goodies - Mostly Complete
Waggy 44 front, Scout D44 Rear, 4.56's, ARB's (F/R) SOA with YJ Springs, 35x12.50x15 BFG MT - Not Even Close to beginning
Also a mostly rust-free 1970 Scout 800A That I'll get to start working on someday...
Chrome won't get you home...BUT Rattle Can Black may just get you back"