I just installed a set of Teraflex adjustable CAs on my 2 door JK with 3.5" suspension lift.
There were two things I need to be careful by installing the new adj CAs; first thing was the pinion and rear drive shaft angle, and second thing was the length of the rear lower CAs.
As the matter of fact, I am still using the stock drive shafts, and my current lift height already made my rear drive shaft angle a little steep. With the new rear upper and lower CAs, I can adjust the rear drive shaft back to a straight line, but that will push my rear axle to the back a little much, however, I was worried about the over pushing the rear axle may cause rear coil springs hit the rear track bar and even cause the rear drive shaft falling down to the ground. Therefore, I adjusted my rear lower CAs a little longer so that I can have a level axle angle; for the rear upper CAs, I kept them as the shortest, in fact, even with the shortest setting, the new rear upper CAs were still 1cm longer than the stock ones.
Here is my rear drive shaft picture, please tell me if I need to adjust it.

 

I only bought rear uppers and adjusted the driveshaft angle straight. With both the upper and lowers in the rear you should be able to adjust both your driveline angle as well as set your wheelbase back to where it should be.

 

It's hard to determine the Pinion angle from the close up pic, but it does appear to be at a relatively large angle.

The tradeoff with the Pinion angle on the rear axle is going to the perches for the coils. As you rotate the Pinion up the Perches will rotate back so you may need to use some coil wedges or adjustable coil mounts to correct them.

Also, be aware that the rear axle moves in a large arc motion so when the rear suspension compresses it swings slightly toward the back. This may cause interference with the sway bar links if you shift your axle backwards too far with the adjustable CAs.

 

Yes, when I was installing the rear arms, I was first adjusted rear lower and upper arms to get the rear drive shaft back to a straight line, in fact, when the rear D.S went back to straight, the rear axle became oblique and so did rear coil mounts, however, I was just worried the oblique coil mounts may not hold the coil springs as tight as before, so that I adjusted the rear lower arms a little longer to make the axle back to level a little bit. Anyway, the new drive shafts are needed as fact.

 

Got 11K miles on my JK .. and mine is more of an angle than that ....