I think I usually end up with the bottom front sides uneven, and have to sand them even, after gluing the two halves together. If you had that section lined up instead of the back it might explain why you have had tailboom issues and I didn't.
I've had one of those side windows come loose, talk about a pain. I ended up shaking it into place then kind of spot glued it with Future. I usually glue my windows with Future anyway so it worked out pretty well, but had me worried for a bit.