Working from memory here, the Instructions called out a fractional sized Plexiglass bit for the canopy. The plexi bits have a different shape that is less likely to “dive” eagerly into your canopy only to bind up and fracture it (the canopy). Find, order, or borrow the correct sized plexiglass bit if at all possible.
Now, for the drill and final drilling then tapping you mentioned, I think that refers to drilling the roll bar, NOT the canopy. I could be wrong, but recommend you re-read the instructions carefully.
All the best for the new year,
First Flight 9/23/16!
No paint yet. Working on a scheme with John Deere colors or accents.