My canapy went on 10+ years ago, and thus I have no clear recollection of how i did it, but I think your observation and logic are excellent. I would make sure you have two drill bits -- a dull one for the plexiglass and a sharp one for the aluminum bow. Figure out the best you can to keep everything in place, then choose one side and drill thru the plexi, change bits and drill the bow. Cleco them together. Go to the other side & repeat. With two widely spaced locations clecoed together, that should minimize the relative motion of the canaopy on the bow. Go back to the first side and do the next hole, then the other side, etc. That should give you the most rigidity as quickly as possible. It's going to be a royal pain to drill plexi with the dull bit, then change to the sharp bit for the bow, then back to the dull bit, etc.. If you have two drills, that would be great. Again, my memory is suspect, but I recall that the plexi bit should also be slightly larger than the metal bit so there is room for thermal expansion and vibration to occur w/o excessive stress on the plexi.