As above, the 2 small dowels might not be aligned, meaning that flywheel isn't on all the way, so it fouls on bellhousing. If this is the case, you should easily be able to see where it's fouling if you take it all apart again!
Once had to grind away part of a mate's bellhousing when fitting a large clutch to a small-block, but never heard of it being an issue on big-blocks..