In addition to missing and misplaced index holes, quite a bit of peel ply and plastic was still on the parts. I peeled, picked and finally sanded at the pieces that would interfere with bonding. Cut the door down to size using a die grinder with grinding wheel.
I used one pair of matching holes to begin the fitting process and worked out from there. I found that a strap duplicator, aka hole locator, to be a valuable tool although the hole marking procedure spelled out in the plans was used too. Clear duct tape versus opaque tabe was also useful.
Spring clamps are a bit too strong and tend to distort the doors. Drilling holes into the top and using clecos worked well along with the clear duct tape at the top.