Rob,
Assuming you have a dummy shaft in the "lay shaft cluster" and the front 
cover back on.....I just flip the trans upside-down and use my fingers to 
line the holes up.  I them drive the real shaft back through.  Remember to 
use a little 300 form-a-gasket on all those shafts and pins where they 
contact the case.
By the way.  I also used a little thick grease to hold those frustrating 
little thrust washers in place for that lay cluster.  They will want to move 
on you.  This is where the fingers come in when "flipping" it over.
Good luck.
 Paul
Colorado
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