If there is the slightest temptation to go to a 35" tire in the future, nut for 4.88's. I went 5.13's with my auto, '05 LJ Rubicon.
DO NOT let the interweb convince you that your D30 won't hold up. Still running a D30 (with Cr-Mo shafts, CTM U-joint's, 4.88's and a Lock Rite lunch box locker).
[video=youtube;Iu_ppJSVhtI]https://www.youtube.com/watch?v=Iu_ppJSVhtI[/video]
Just an example of the regular abuse my D30 has been through. You have to remember that you have a D30 and not a D60, and drive accordingly. Those are 36" bias ply Interco TSL's on 15" Cragar steel beadlocks, probably 65 pounds per wheel tire assembly.
If you upgrade the shafts in the D30, do NOT buy into the increased spline count hype. Get some Cr-Mo shafts, 760x joints, and call it a day, save your old shafts for spares. If youincrease the spline count, the only way to get spare shafts is to buy two sets of CUSTOM shafts. Break a stock spline count shaft, no spare, any auto parts store is your friend for a new stock spline count shaft!
Just for the record, I swapped stock TJ shafts into my YJ D30 to replace the 2 piece shaft/vacuum actuator on the YJ D30, abused the stock TJ shafts for years before finally breaking one and upgrading. (It broke at the U-joint yoke, same place they all break, making the spline count thing useless, or cool interweb build stats).
Look for a take out D44 at your local 4WD shops for people that have upgraded. It's a bolt in application, bonus points if they have the driveshaft to go with it! I'd go with a plain D44 rather than a Rubicon D44, you MUST use the low pressure air pumps to engage the factory air lockers on a Rubicon D44, there is no reliable way to regulate OBA down to the 5psi required for the factory lockers of that era. Plain Jane D44, you get locker of your choice.
Seems like there aren't a lot of us YJ/TJ?LJ guys left. I've got a YJ and an LJ, made/learned from a few mistakes on the YJ. Corrected most of them on the LJ build.