The devil is going to be in the details. You went from 3.07 gears to 4.88 gears…that is a 58% increase in driveshaft speeds at any given vehicle speed. You mentioned “above 50 mph” as a data point early on in the thread, so I mapped out your numbers. At 55 mph, your driveshaft is at 2835 rpm. With 3.07s, you would have had to go 87 mph to achieve the same driveshaft speed.
While you also have the lower speed vibrations with the clutch disengaged now, that could also be just because your speeds are much quicker now than they were before.
So with 3.07s, how fast did you drive? If you putted around, you likely didn’t reach the problematic driveshaft speed points.
Back to the subject of the regear - why were all the bearings diagnosed as “shot”? If that were true, then then redoing the work should have fixed it. Sounds like a Hail Mary attempt and that maybe the bearings were okay.
At this point I would remove the rear shaft, drive in FWD, and reevaluate. If problems go away, you know where your problem is. If they don’t, you don’t. Removing the front shaft made no difference, so I would assume your front is good to go and there *should* be no vibrations if you drive without the rear shaft.
You can park it but unless you simply have no time, there’s no real reason this can’t be fixed or dramatically improved.