Tonight I spent some time grabbing measurements to try and figure out where suspension will end up. I made a basic outline of the TJ frame, the front section isn't exactly right since I didn't bother drawing the pinch in, but the rest is reasonable.
Green lines are the frame rail for a stock TJ, red lines are the axles, and purple lines show where the links will fall. Front links are all 36" long, rears will be about 40" long.
With how close the uppers and lowers fall, I'm trying to figure out if I want to go the lazy route and make brackets with the uppers and lowers directly over one another like many of the DIY brackets are.