It doesn't sound like you personally installed your SYE kit, so it's possible that who did install it may not have set the rear axle's pinion angle properly. An improper pinion angle will cause drivetrain (u-joint) vibrations.
The pinion is that shaft that comes out of the front of the rear axle and connects to the driveshaft. If that pinion shaft's angle does not match the CV driveshaft's angle (see below) that was installed at the time of the SYE kit, it will cause vibes. Is there a chance you can post a photo of where the rear driveshaft connects to the rear axle's pinion shaft, taken from the side so we can see the angle? A second photo showing the front of your rear driveshaft would be useful too, to confirm what kind of a driveshaft is actually installed, to confirm it's an aftermarket CV (constant velocity) driveshaft.
If your rear driveshaft is indeed a CV driveshaft as indicated by a single u-joint in the rear and two u-joints in the front, you angles should look like this...
Finally, you should not still have a transfer case drop if you have a SYE and replacement CV driveshaft installed. Having the SYE and CV driveshaft installed eliminates the need to still have a transfer case drop installed.
Once we have a couple good sharp well-lighted (use a flash!) photos of the rear underside of your Jeep, we can probably help figure out what is causing your vibrations.