Great questions. Not everybody does this the same, but...
1) What did we do about fit on side skirts and such?
Essentially you're asking about whether and how 3/8" thickness rule is applied around the full circumference of the canopy. In my case, I have the required thickness at the front and along 95% of the rollbar. The canopy and rollbar slowly converge to touching at the longeron, so the amount of glue at that juncture is thin. Same for the side skirts. I have no screws on the side skirts. I did put primer and glue in the slot between skirt and canopy rail, but it's just a thin layer. Am I concerned about bonding strenghth or structural weakness? Absolutely not. In these areas, the skirt/rail structure and the thin layer of glue on both sides of the plexi provide a lot of combined holding force. On the rear canopy, I also put a thin layer of sika around the back edge, but I'm relying on screws to hold the rear glass in place. Of course along the roll bar, it's all sika as with the front half.
2) How do we make sure the front and rear are flush?
During the trimming/fitting process, I tested the fit of the front/rear halves with some shims taped in place along the roll bar. Then in the gluing phase, I glued the front canopy first. When I glued the rear canopy, I checked the "flushness" immediately after gluing. I found it necessary to adjust the shims here and there to get everything flush, and I found it helped also to tie a strap across the canopy (hooked at the rear spar on both sides). With the strap in place, I could add towels here and there to adjust the pressing force on specific parts of the canopy.
I found the canopy installation to be the most fiddly, least enjoyable part of the project. Definitely one of those 'earn your stripes' kind of efforts. Now that it's behind me, I'm satisfied with the result, and all that sweating over unachievable perfection was worth it. One funny thing is that when I see someone posting a picture of a bird-strike, I'm immediately traumatized at the thought of ever having to redo a canopy, and then my second thought is the much more important stuff like hoping everyone is ok and wondering what it would be like to land a plane with bird gore all over and a giant hole in the plexi.
http://donka.net/gallery/rv7canopy/DSCN0199_001