Well, not being familiar with your "specialist's" computer program, it would be hard to comment on what he was trying to accomplish, but let me guess, the program is intended to deal with stock drive lines, not custom creations. If you had a stock drive shaft, you would have two u-joints, one at the T-case, one at the pinion. These joints would have to be kept close to the same angle to keep the joints running in the same ellipse at the same speed. A computer program could do something like this fairly easily because it is just math. Each joint in a standard drive shaft should be at an equal but opposite angle from its mate.
The double cardon joint creates a zero angle at the output end of the joint, regardless of the angle at which the shaft lies at rest. Some folks refer to these as constant velocity joints. Because the double cardon leaves the drive shaft without any joint to joint speed matching issues, putting an angle on the pinion end joint defeats the purpose of having the double cardon by creating a drive shaft with ONE joint running without another to balance out rotational variations arising from the design of the joint. The farther the pinion end joint is from zero the worse the vibrations, so when your specialist cranked in additional pinion angle, he made matters worse, not better, assuming that when he added shims he pointed the nose of the pinion down instead of up.
The pinion shaft needs to point straight at the output end of the double cardon joint. This almost certainly will require pointing the pinion UP from where it was when stock. Most shims cause the pinion to point DOWN when installed as intended. If this is what was done with your vehicle, you may be able to mitigate the misalignment by installing the shims the other way around, but best to get under your ride and take a look to see which way the shims are installed, and how much of an angle the rear joint is running at. Check for running angle with the car normally loaded and the tires on the ground, not hanging in space, which should put the drive line somewhere in the middle of its range of travel.
You can lift a vehicle to such an extent that joints run at 20 to 40 degrees without creating dangerous vibration if you use the right joints. With your small degree of lift, you should be not more than 10 to 20 degrees at the double cardon, which should be within the range of a standard joint (I believe a standard double cardon will run at around 30 degrees without binding), and near zero at the rear, which obviously is within range of any u-joint. If your guy set up the pinion so that it too had 15 degrees of tilt between pinion shaft and drive shaft, it is already close to its working limit, and could bind, depending on the exact joint used. There are high-clearance, high angle joints out there, but most folks don't use them. Or to put it the other way around, those who do use them also know how to build a proper drive shaft.
Anyway, the safest and easiest way to realign your pinion will be to reset the spring perches, which requires taking the axle loose from the springs, cutting off the old perches, and welding on new ones after grinding off the weld lines. Shims are okay for verifying new running angles, but I really don't think they are a best option for long term use because they can and do wear, they can shift around, and they can pop out under stress, which can lead to parts failure in bad places when the u-bolts go loose from loosing a shim.
Thousands of Cherokees have been successfully lifted with no drive line issues, so have faith that this can be worked out, probably for the price of a pair of perches, obtainable from truck and trailer supply houses, and a few hours of time and effort with torch, grinder, and welder. If you don't have these tools, find someone who does. Lots of time, these changes can be done for the price of a case of brew, and a few hours with a couple of buddies.
If you have access to a digital camera and can post a few shots, why not post some photos for us to see, and perhaps it help to illustrate the problem.
