B16 trans on a B18B1 block, crank won't turn when trans bolts are torqued, take off the bolts (or loosen them) and the crank turns along with the diff.
Also, I tried removing the trans to take a look at the clutch and flywheel in case there were any clearance issues and the trans wouldn't come off at all

 

reseat the transmission properly, but then again you probably fucked up the clutch...

 

All the bolt holes line up properly and same with the input shaft, I can't think of a more proper way to line up the transmission.

 

Realign your clutch it's most likely off and binding on the casing