Measure from the face of the transmission to the end of the input shaft and record that measurement. Then measure from the inside of the crank hole to the mounting face of the bell housing and compare the two measurements. This will tell you if the crank hole is deep enough to accept a full length input shaft.
As already stated some auto cars with cast cranks weren't drilled or weren't drilled deep enuf for a pilot bushing. That was the case when I did my 727 to 833 conversion. I ended up using the larger pilot bushing available from Brewers Performance that fits in to the converter snout on the crank....so that solved that.
I still had the issue of the input shaft being too long so I ended up cutting a little off the input shaft of the transmission as well with no ill effects. A lot of people will say no way, don't cut the input shaft but its not a problem. There is still plenty of the input shaft being supported thru the pilot bushing.
Another tip is this, I had to do this as well for the same issue you are having (cant get trans to fully mate with bell housing) even after cutting the input shaft and knowing for a fact it wasn't too long. Loosen the pressure plate mounting bolts before trying to install the trans. Those plastic clutch alignment tools (I assume that's what you used) that come with the clutch kits aren't as tight fitting in the clutch disc splines as the real steel splined shaft is....so loosening the pressure plate mounting bolts allows the clutch disc to "float" and move some.....this is what worked for me when I couldn't get the trans to fully mate with the bell housing after 4-5 attempts.
