Trimming canopy

I have the canopy drilled to the frame and need to final trim the rear and sides. Is it acceptable to do this while it is clecod to the frame or does that put stress on the canopy as you cut it?

If you wonder why no holes near the rear top section.... That area is going to need some spacer blocks. I am still contemplating how to get these holes in the correct place over the center of the frame. Anyone go through this process and have a good plan?

How far away is the plexi from the frame?

The widest spot is 7/32nds. Van's said to either leave it as is or put spacer blocks in-between. I would leave it but wonder if the open area gives the plexi too much expansion in the that area and could put pressure on the nearest fasteners?