Have you tried moving driveshaft yoke as it enters rear of transmission up and down to ensure no slop at this bushing. Unlikely the cause but certainty the cause of unexplainable vibrations from driveline cruising down the freeway.

Slim chance of your problem, good news is easy to check. Should have no movement if all is well and snug.

Back to your original title, has bellhousing been throughly dialed in! Running out of ideas, had considered that, but assumed had already dialed in when replacing clutch. However do not see anywhere that it had been.

Wonder if mainshsft bearing out of transmission into clutch might cause your shutter if sloppy. I believe you said had replaced pilot bushing/bearing.

Are rear of transmission and differential shafts running true and straight left to right? You have mentioned that driveline angles are ok up and down. Am assuming U Joints are in order.

I had missed earlier comment that you had checked driveshaft for proper length.

Are you certain that rear springs are quality products with correct number and positioning of leaves. Rear axle properly positioned in springs?

I would think that a tweaked pinion shaft would cause a wealth of issues besides a shudder in low gear,,,,vibrations, broken u joints etc.

Interesting no issue in reverse,,,takes me back to engine mounts. Is engine setting at proper height in K Member. Not one side higher than other or tweaked so tailshaft from trans is not pointed directly left/right to pinion at rear,,,same as mentioned earlier in this post.

With hood up, can an observer see shudder in engine?

If you just slip the clutch gradually to move forward in low,,,,do you still get shuddder. If let out rapidly with sufficient gas not to stall, will you have shuddder starting in 2nd.

Wonder what you might see on a chassis dyno with full weight of rear wheels on the roller.