If you had the transmission hanging from the input shaft when you removed the engine, you may have bent the center section of the disk, which would cause it to drag on the flywheel and pressure plate. Not real likely, but a possibility. Did you put in a new pilot bearing in the flywheel? That may be hanging up, causing the gears to turn even if the clutch is disengaged.
I think you will need to remove the trans in any case to figure out what's wrong.
Also, if you backed off the clutch linkage, you may have caused the linkage to not have enough movement to totally disengage the clutch when the pedal is to the floor. That would be the first thing I would check. Adjust the linkage to spec (the pedal should have just a little play before the throwout bearing contacts the fingers on the pressure plate.)
BTW, 90W isn't thicker than 90W/140. The 90 weight will actually be thinner when warm than 90w/140, which has viscosity index improving additives to keep it from thinning out as much when warm. It acts like 90w when cold and 140 when warm.
I hope you can get the grinding issue figured out.
