Well, the promotions/ship building system is currently under revision (v. 5.0 gives just the current state of things), you guys might want to check out the MOO2Civ subforum. (And I'll see if I can copy/paste that post to over there to join in the discussion.)
BTW, the forum is over here:
http://forums.civfanatics.com/forumdisplay.php?f=354
As for the Civilopedia: it's indeed "underdeveloped" at the moment (most entries are simply missing). The problem is that the current version isn't the definitive one, so a lot of further changes can be expected. But any gameplay feedback is most welcome, so thank you for that (as far as the mod let you...).
That's... disturbing. I thought the can't-build-buldings-on-capture bug was squashed by now. I don't suppose you have a savegame or logs.zip to go with it?