More canopy work tonight. Drilled and cleco'd the aft bows. After I got that done, I felt more comfortable tackling the sides of the plexiglass. They were overhanging the side rails by a long way, but I didn't think that I could accurately locate the cut lines until I had it all pinned down.
There is a joggled strip that receives the side of the canopy (last pic). The plexi is sandwiched between that strip and the side skirt and screws pass thorough both bits of metal. The side skirt is then riveted to the the side rail. Clear as mud, probably.
I wanted to locate the cut lines so that there is enough plexi to have good edge distance, but not so much that I had to trim slivers away with the die grinder. So, what I did was clamp the joggled piece to the outside of the canopy with the bottom lined up to the bottom of the side rail. I struck a line and measured down to where I wanted the canopy plexi to end (inside the joggle and skirt sandwich) and struck the cut line. It worked out pretty well and wasn't overly complicated to do.
The last pic shows the joggle positioned on the sides.
