Kind of depends on your expected level of off roading and technical/mechanical expertise;
An AX15 is my favorite manual transmission... Got an auto in the '06 and it really detracts from my off road enjoyment.
A fuel injected 4.2 was one of my favorite engines (but injecting it, successfully, was a, relatively, major project). The 4.0 will already have fuel injection (and thus no carburetor problems).
Suspensions mods and axle changes will be necessary with both YJs and TJs to fit large tires.
The YJ will need the rear wheel wells trimmed and perhaps an axle relocation along with TJ rear flairs to fit 33" tires and keep the center of gravity low.
35s will need body butchery and rear axle changes to assure reliability a long with relatively large lifts(raised center of gravity)
I believe that tummy tuck kits are available for both (assuming you are not able to fabricate. Gives additional break over clearance without the need for excessive tire size.
For light to moderate wheeling on 32 to 33 inch x 12.50 mud tires I would go with the TJ('03) and a bout a 2-3 inch spring lift; drop in at least 4.11 gears (junkyard axles available) and, eventually, some alr lockers or Torsen style limited sllps and you will be pretty well set.
For light trail riding, stock, the TJ should only need (close to stock diameter) mud tires. Many here seem to favor all terrain tires but I have found them good mostly for street use (off road, they do not give me the traction that I look for).
Enjoy!
