I assumed that this is why the original mount had no top studs (put bolts in after you slide it in place). I found out the hard way that the newer mount with the top studs would not fit. I did consider shortening them but I decided that drilling different holes on the chassis side and using an NOS 36 mount was better. In retrospect, it might have been better to try what you did. I how have holes for either mount.
Regarding the crank. I did notice that if I wanted to remove the crank pulley I would need to jack up the engine a little to get on the nut. Gaining access with the hand crank did not occur to me. I am not sure if mine lines up well enough. I suspect that I would have the same problem as well. I don't anticipate using the hand crank but eventually I will want to try it or at least try and remove the crank pulley. How thick are your shims, about 1/2 inch?
Rebecca