yeah i think im going to get the adjustable trac bar but then wont i need to get another alignment when i adjust the trac bar to the correct length? i just got done with the caster, i shortened the control arms until my diff tilted 4-5 degrees from the way xjbubba said. i think my toe-in off a little bit now so im going to go out and measure that and try to get it close.
First, hopefully you discovered that you should ADD the calculated correction to your current pinion angle--NOT subtract it, like I said in my previous post (post #5 of this thread). As you know, you want to decrease the caster angle of 10.6 to ~6*--this would mean you rotate your pinion upwards the 4.6* needed. Second, changing the pinion angle affects u-joint operating angles. Not sure what u-joints your Jeep has, but constant velocity type joints--mine is a "double Cardin"--stock '88 with part-time transfer case--which requires the u-joint at the diff to be ~.5* positive--meaning the pinion points slightly above the drive shaft angle.
A problem with lifting a Jeep is the u-joint operating angles get out of whack, and can cause front drive shaft vibration, especially if your front axle is always connected to the transfer case. You can correct for this by using adjustable control arms, as you're doing, but as you know, you will be changing your caster at the same time. So, you have to decide on the compromise you wish to make--maximise caster angle, or drive shaft operating angles, or some where in between. At 3" of lift, the compromise is generally not hard to live with. At 6" of lift,the affects of "compromise" are a lot harder to live with on a "daily driver". The real solution is to cut the inner "c's" loose on the axle housing, and rotate them to adjust caster after the pinion angle has been set. People normally do this when they build an after market axle.
Adjusting caster does affect toe. Incorrect toe is probably one of the worst conditions you can have as far as tire wear; it will also cause "darty" behavior on the highway, so by all means, correct your toe to factory specs, or slightly in--like ~1/8 inch.
If you are set on doing a 6 inch lift in the future, I would not buy an adjustable track bar now--they generally are cut to lengths with available adjustment for a given lift--like 0 to 3", and 4 to 6", etc. They're not cheap, so it's wasted money to buy one you know you are going to get rid of in the near future. A 3" lift should not require much change in the track bar length.
Measure how far the driver's side tire extends past the flare, verses the passenger side. I wouldn't worry about 1/2 inch difference.
I don't think changing the track bar length will affect your alignment, but it will affect steering wheel centering.
Also, I wanted to wish you good luck at boot camp--it will be an experience to remember!!