Shaking while coming to a stop in gear

Does this happen at all speeds? If you put your foot on the brake at 60 mph while in gear does it still shake?

Does it make a difference if you are touching the brake pedal or just engine braking?
 
Engine braking and when I'm accelerating in 3rd and 4th it shakes alot too then over 60 it still vibrates but not as bad
What rpm ranges are you engine braking and accelerating? 3000rpm?

What is your tire size, transmission and axle gearing?
 
Transmission / engine mounts perhaps? It's worth visually inspecting them.
 
I don't know, it still sounds to me like it could be clutch / flywheel shudder. Happened on an old VW of mine back in the day, and the symptoms were similar.

I also think you should visually inspect the engine mounts and transmissions mounts, as that's easy to do, and would at least rule that out.
 
If you have a lift your pinion angle may be off. I had the same problem on my yj. If the pinion is too high, you will shake under both acceleration and decel, if it's too low you will shake only on decel. The angle should be around 21-23 degrees I believe.
 
Front drive shaft? It appears the problem happens when the DS is under load. Either from engine power or the wheels powering back to the transfer. Pull the front shaft and see what happens. Also give a good look at front axle Ujoints. They can also vibe when one side of the front is applying more load than the other side is.