When I was in college my part time job was at a company that built abrasive belt sanding machines. While I was there I learned sooo much about machinery and the nuts and bolts of assembly.
Here's something to try that applies to anything that attaches with more than on bolt/screw.
Get everything aligned and test fitted. In your case you'll need some sort of alignment tool, dowel, pto shaft or even a half inch socket drive extension. Install the screws that hold the bell housing starting at noon, no you don't have to wait until lunch time...then go to the opposite and work around in the same direction. Just finger tight at first. Check alignments. Now, snug up the screws the same amount using the same pattern. Check to see if the clutch plate is still aligned as you go. Do this in stages until its time to torque the bell housing screws.
One time I had to keep a shim plate aligned with the base of an assembly. think of a metal gasket. To keep the two aligned I used string tied through the bolt holes to keep them aligned. Once I got all of the bolts started finger tight I snipped the strings.
Have fun!