you say stock drive shaft. Most were CV joint drive shafts which are good for high angles....but they are weak so generally not the best shaft to be using with a 4L and big tires. That will really stress it so I wouldn't be surprised if it has gotten damaged.
It is also possible that the shaft was already going bad A clicking noise, particularly under heavy load is when it shows. I experienced this mostly in first gear, but only when accelerating hard. You experience with second or 3rd gear still seems consistent.
Some were manufactured with regular u-joint drive shaft in the rear The u-joint ones are stronger. Also unless you have had this BII a long time it is entirely possible it was previously replaced with a u-joint type.
With a u-joint shaft you could have issues with with just a bad u-joint That can cause clicking as well. The lift will create added stress. The reason CV shafts were used in the first place was because of the high angle. A u-joint shaft does not turn at a constant velocity and relies on the angles between transfer case and drive shaft matching the angle between drive shaft and differential input. That way the constant velocity output becomes non constant in the shaft and returns to constant at the wheels. If the angles aren't matched well enough there can be vibration. Any vehicle manufactured with a u-joint has that set up. The stock BII wasn't often set up that way due to the CV shaft. On mine I swapped in a u-joint shaft and while angles aren't really right, I only experience vibration under hard accel in first gear.
Anyway even with angles correct, as the angle becomes steeper the drive shaft speed variation becomes larger and larger and just the accel/decel every rotation can cause some vibration. That is a vibration so not a clicking. Just making you aware of this. By the way some amount of angle is needed for drive shaft to work properly. If you try to set it up strait with no angles that works fine until you load something in the back or go over pumps. That will cause vibration to occur.
So first step is figuring out what sort of shaft you have. If a CV shaft there isn't much you can do other than replace it. I have heard people being able to go to shops to get them rebuilt but not many do that. With the 4.0L and big tires it will fail eventually anyway. Also if you are going to upgrade give serious consideration for a double cardan type shaft instead of a simple u-joint shaft (more info on that further down). I have not found CV type replacement shafts. I just have stock setup and drive road and would prefer a CV type, I haven't found one yet.
If a u-joint shaft, you may just have to get the u-joints replaced on it. Not a big deal.
I forgot to mention, with the lift your shaft will probably be extending further. Make sure you have enough slip joint movement. That shouldn't cause a clicking related to shaft rotation like a bad u-joint or bad CV joint. If it clicks it will be related to hitting bumps.
If you have vibration issues with your new setup, you might need to go with a double cardan type drive shaft.
The double cardan shaft has a double joint at one end and a single at the other. The double joint goes at the transfer case end. This type of shaft can work with high angles and can be as strong as the u-joint shafts.
I don't know how long the vehicle had the 4.0L in it The additional torque of the 4.0L especially with the large tires puts much ore stress on the drive train. As I mentioned the CV type shafts probably won't fare well at all as they are known to fail with stock setup like happened in mine. The transmission, transfer case and differentials also get stressed. Do you know what you have for those? I don't know if the transfer case is at risk, but I know many go for the upgraded trans and differentials to handle the load As an 89 your BII may already have the heavier duty versions. Just something to look into.
