I'm no expert , but I am researching the same issues. Dana 44 or 8.25 makes the angle greater between the Trans Case and rear end due to the rear end housing being longer than a Dana 35. The distance from output shaft on Transfer case to Rear end on your setup is shorter than an older XJ I have come to believe through research.
I am about to do a RE 3.5 lift and also have a 8.25 rear end, If I had a D35 I would not need a SYE and TC drop would probably work. lots of people ask about if they need a SYE and some people say it really depends on your XJ. It really depends on your parts actually.
Here is a good one , Anyone with a 8.25 or D44 231 TC get theirs to work without a SYE ? with reasonable TC drop ?
It's based on your XJ, not your parts. The parts will change things slightly, but not enough to make a significant difference. For example, if your driveshaft is 29" long and stock, axle yoke is 3" below the transfer case output, you would be at an angle of ~ 6*. If you do a 3.5" lift, now the yoke is 6.5" below the output shaft and you have an angle of ~ 13*. If the d35 has a shorter nose by 1", you could have a 30" long driveshaft. At 3.5" of suspension lift your angle would be ~ 12.5* instead of 13*. Not much of a difference.
These numbers are all made up, but should be a decent representation. My point is that your lift height will have a lot more to do with the angles than your physical drivetrain components unless you have a d35, rear stretch, and a manual transmission or something, each of which would contribute to a longer driveshaft.
An actual example is that my 2 door 5 speed XJ with the Chrysler 8.25 had 6.5" of lift in the rear with a 1" transfer case drop and ran the stock rear driveshaft with no issues whatsoever. Ran on the highway at 75 mph smooth as butter. My roommates 2wd XJ with the crazy long rear driveshaft got a vibration with a 2" budget boost, even with good u joints. Some Jeeps just handle the changes better than others.