OK, we can eliminate the engine and the transmission input shaft from the discussion. That leaves the rest of the tranny to worry about.

Hmmmm.... Of course the tranny output shaft and beyond rotates with road speed, not engine speed, so the 3000 RPM mark would be irrelevant. Sounds like the issue would have to be in the tranny itself, specifically something to do with the meshing of the gears.... I guess... Hmmmm....

Yeah, I'm thinking the countershaft (aka layshaft). It spins in sync with the engine and input shaft. But it also spins in neutral???

You could still have a bad U-joint in the driveshaft or an improperly installed one, happened to me once. Also when you took it apart to install the RT mount did you match mark the flanges before you removed the driveshaft ? sometimes they only work right one way. You could try reinstalling the driveshaft in different positions and test drive it and see if you notice a difference.

Have you checked your half shafts? Mine seems to be loose, it could be the inner wheel bearing.