Matt-
The links don't need to be mounted on the same plane as the T-case output. You can control driveshaft angle with the link location. My rear u-joint angle changes less than 2 degrees from full stuff to full droop with 14" travel shocks. Macgyver and I have similar set ups with the uppers triangulated and converging above the diff. All four of my links are 40", the uppers mount ~3" higher, and ~5" behind the lowers. I'll run a center mounted limiting strap, and let the captured coils control the droop at the wheels.
The axle mounts also have a great influence on geometry. The lower the LCAs are on the tube, the less torque stress they have, but it will increase the angle of the arms and raise anti-squat. Many "experts" recommend at least 6-7" of vertical seperation of the links at the axle. In general, the flatter you can mount the arms, the less AS you will have. Keep in mind, some AS is good, but too much can cause wheel hop, resulting in a loss of traction. The early generation Tereflex long TJ long arm kits had long lowers with short uppers. The resultant angles produced too much anti-squat, and also caused to front to "jack" and loose traction on steep inclines.
Also be aware, I am by no means an expert. This is my first attempt at suspension design, and all my work is based only on theory. I don't even know how well my junk will work when I get it completed. I have done as much homework as possible, but take my opinions with a grain of salt.
-Jon