Ambitious project you have going on here...and very impressively executed thus far. Nice work!
Regarding the rear canopy fit, a few different possible solutions come to mind...
First, check the fit of the original kit canopy. Trumpeter's accuracy woes are well documented, but their fit of parts is generally excellent, at least from what I've experienced. If this is the case here, then you could graft the rear canopy section from the kit onto the Zactomodels frame.
Another method might be to cover the aft canopy contact points of the fuselage with thin self-adhesive aluminum foil, place the Zactomodels canopy into position, and carefully press small "worms" of Milliput (or other epoxy putty) into the crevice formed by the ill fitting frame. At this point, don't be too concerned about excess putty on the outside. Just be sure that the gap is fully stuffed with putty. After the putty hardens, sand away any excess until the parts are flush. Gently pry free the canopy from the fuselage (the putty will not adhere well to the foil). Lastly, peal away the foil. If all goes well, you should have a nice fitting piece in the end, the epoxy putty having formed a new edge that matches the fuselage opening.
Yet another approach would be to glue into place the Zactomodels canopy frame, fill and sand smooth the entire gap, and then restore the hinge line with careful scribing and/or etching using a needle and/or micro saw.
Good luck the rest of the way. I'll be following your progress.
Edited by allthumbs, 05 July 2017 - 11:40 AM.