I masked the canopy and paint leaked through. how do I remove paint from the clear parts of the canopy?

Same as with scratches. See my response in this thread: https://armorama.kitmaker.net/forums/28310&page=1

It depends how bad the the problem is. It may be possible to remove the paint with a wooden cocktail stick, cut to a chisel point, and push at the paint. If you try this it may be wise to run a scalpel around the frame edge to seperate the paint on the canopy, from the paint on the frame. Scraping like this isn't as scary as it sounds, the clear plastic is harder than the wood. If you go carefully you wont scratch the clear parts. There maybe a slight "hazing" but a brushed coat of Kleer (Future) will clear that up. I have done this several times, with no problems.
Mal