I think as one of the ways to tackle this canopy / windscreen issue while maintaining the relationship between the canopy and windscreen is to temporarily glue them together with PVA or perhaps masking fluid. Once this is setup then see what can be done to the fuselage where the canopy sets. It may also be possible to modify the clear parts a small amount.
By having the two glued together temporarily, you don't have to worry as much about the fit between the canopy and windscreen when you have to remove clear plastic. You can test fit the entire assembly as a single piece.
Steve (@sjcorvi), thanks for sharing this information. I have tried using thicker UV resin for some clear part work, but this putty has a thicker consistency which will be useful.