Welcome to the club!!!
Unfortunately, it could be anything from the harmonic balancer to the rear axle.
If you have it still apart to change the pilot bushing, I'd take the flywheel and clutch assembly and have it balanced. If the flywheel has been resurfaced, the balance characteristics have changed. Aftermarket clutches aren't the most well-balanced items either.
Before you assemble the clutch together, place the cover and disk on the flywheel and clamp it down. Notice the height of the diaphram where the throw-out bearing would sit, as on top of the fingers. If they aren't within 1/4 inch of all being the same height, get a new cover(pressure plate).
I'm sure before disassembly, you've taken and placed the car on four jack stands, two of the stands are on the rear axle tubes, so as to give the proper pinion angle and slack in the driveshaft, and placed the trans in first gear at idle and watched the driveshaft turn straight and true, if not, then U-joint replacement is in order.
Another thing you met do later or before tear down is to do a compression check of the motor to make sure the eight cylinders have the same compression. Usually, if one is low, it will vibrate the driveline.
I hope these well help some and gve food for thought, others here will have some good suggestions.