When I had a RE 3.5 on my TJ seems like I had the lowers about 5/8"-3/4" longer than stock, which jives with the chart.
Use the chart as a guide but fine tune the lowers to get the wheels centered back in the wheel well, in the stock location. Use the front UCA's to get the caster set correctly once the LCA's are fixed and use the rear UCA's to get the pinion angle set correctly once the LCA's are fixed.
Yep
The most important thing is to learn why they need to be the length they need to be. That chart is a good way to get started but thats it. Do a little reading on caster angles and alignment in general. IMO the worst thing you can do is go on a board like Jeepforum or the like and read all the crap guys who really know nothing preach.
Like Foreman said, set the length of the lowers where you like how the wheel is centered in the fenderwells. Take into account the steering from lock to lock to make sure the tires dont rub on the quarter panels or bumpers. Get the lowers set how you like the tire placement then measure from front to rear axle on both sides to make sure they are parallel with each other. Then diagonally from front to rear axle. This measurement may differ some from side to side depending on how well the trac bars are matched to the ammount of lift. There isn't a whole lot you can do to fix it unless you have adj. trac bars.
Do yourself a favor and buy one of these
http://www.harborfreight.com/dial-gauge-angle-finder-34214.html
Now that you have those 2 measurements right you're readyt to adj. the uppers to set caster on the front wheels. Clean the top of the upper ball joint so the angle finder will sit nice and flat on it. adjust the upper arms in or out to get the angle finder to read 5, 6, or even 7 deg. positive castor meaning the upper BJ joint sits to the rear of the lower BJ or the axle is tilted back. Caster angle is what makes the jeep track straight down the road and brings the steering wheel back to center as you complete a turn. The wider the wheel and the less backspacing the better it is to have more caster to counteract the leverage they put on the steering. "Scrub radius" is a good term to Google that will help explain why the taller wider tires/wheels put more leverage on steering components.
In the rear the uppers will determine pinion angle. If you DO NOT have a SYE and no CV rear shaft installed in the transfercase hopefully you have t-case drop brackets. Take the angle finder and figure out what angle the output shaft points down at. Once you have that put the angle finder on the pinion yoke and adjust the uppers in or out until the pinion points up at the same angle the output points down. If the case is down 5* then the pinion should be up 5* This is usually hard to make work on a TJ due to the short rear d-shaft and the steep angle it sits at with a 4" lift. If set up correctly the shaft will pretty much bind with any ammount of rear droop.
If you have a SYE with a CV rear shaft (which I strongly recommend) adjust the uppers to get the rear pinion to point directly inline with the driveshaft.
After you've done all of this you need to go back and take the two initial measurements again to be sure that both axles are still square under the jeep. If not adjust accordingly. It may take a few tries to get it all right. It's best to have a buddy who can help with the tape measurement. Oh and most importantly do this all on flat ground with the jeep sitting level front to back and left to right or you'll get false measurements with the angle finder.
