Does it grind if you choose 2nd before you put it in 1st and just so we're clear, it will go into gear running?
No synchro on first gear so if the input shaft is turning at all when you pull it into first or reverse, it's going to go crunch.
If I had to guess, and this is assuming the clutch disc isn't stuck to the flywheel, the input shaft is dragging in the pilot bushing a little. If they replaced the input shaft when they rebuilt the trans, it could be as simple as letting the new pilot burnish itself into the old bushing.
I'd adjust most or all of the free play out of the clutch to maximize disengagement air gap between disc and flywheel, and see if that helps before I got into pulling things apart again.
Kevin