Here's a letter I wrote for a fellow MJer last week. It might give you some ideas. (or if anyone sees any mistakes in the details, lemme know) The list was for a 2wd to 4wd conversion and a stick, but the important upgrades are the same.
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A Blueprint for 33s:
-MJ/XJ front axle
--non-CAD axles are preferred, but the CAD axles can easily be retrofitted with a 1-piece passenger-side axleshaft from later model Jeeps.
--95 1/2 and newer will have Dana 44 U-joints (297s) in them, but all older years will accept them as a bolt-in upgrade
http://www.madxj.com/MADXJ/technical/technicalfiles/ARD30shafts297andSeals/D30shafts297andSeals.htm
--97 1/2+ are low-pinion are not desirable for that reason (and newer axles cost more than older axles anyway)
--99% of all front axles from a 2.5L equipped MJ/XJ will have 4.10 gears and are the same axles used in 4.0L Jeeps
-MJ/XJ front driveshaft
--Look for one with a CV joint at the t-case end. I thought they all had this, but apparently not.
--The ones on 2.5L Jeeps might be slightly shorter, so be sure to measure before you buy.
-Transmission
--AX-15 from 91-94 will bolt-in directly with no changes to the slave cylinder assembly
--95 and newer will have the more desirable external slave cylinder. Both units work fine, but the external will allow repairs to be done to it without dropping the transmission.
--95 and newer will also require the newer clutch assembly
-T-case
--it's best if you can find one still bolted to the AX-15, that way you'll know the spline counts are the same. Otherwise, stick with 91+ t-cases that came from behind 4.0Ls, as I'm not sure when exactly the change from 21 to 23 occurred in 2.5L equipped Jeeps. If you find one for a good price, you could always count the input shaft.
--a 23 spline MJ/XJ NP-231 will bolt right in
--a 23 spline MJ/XJ NP-242 should bolt right in and allow 4wd on dry pavement (not all that necessary in Florida ;-)
--be sure to grab the t-case linkage including the bracket that bolts to the underside of the Jeep
--A slip yoke eliminator is a wise investment
-Rear shaft choices:
--have your current one shortened to the proper length (will not work with SYE)
--find an MJ shaft from the junkyard that fits your application (this depends on the lift involved and this will not work with a SYE)
--have a new one made
-Rear axle
--Please do not put any money into your Dana 35 if you want to run 33"+ tires (just my opinion of course, lots of people do with varying degrees of success/failure)
--Ford 8.8 from behind a 95 and newer Ford Explorer equipped with a V8 (should have 4.10 gears, disk brakes, posi-traction, 5-on-4.5" bolt pattern, and be easy to find) You will need to weld on new spring perches, but that's necessary for all lift/axle configurations except keeping the MJ's current axle spring-under.
--Dana 44 from an MJ/XJ (drum brakes, requires regearing, may have posi but it'll be a really old posi that probably needs a rebuild, and can be tough to find)
-Lift
--at least 4.5" is needed to clear 33s (and that includes a lot of fender cutting up front)
--Extended bumpstops are your friends!
--you could always do a 3" lift with some aggressive 31s for now, then upgrade the lift later on. There's no need to go super-big right away. 33s only provide 1" more ground clearance than 31s, but bring a lot of complications with them.
This set-up will give you everything important (4.10 gears to help match your tires, Dana 44 U-joints up front, 31 spline axleshafts out back).
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Jeep on!
--Pete
MJ Yahoo Group:
http://autos.groups.yahoo.com/group/jeepcomanche/