3 bugs I've found;
1. You can still build academies with a great scientist, after you've researched computers and supposedly obsoleted the academy builds.
The Academy (also Scotland Yard, but it never goes obsolete) uses a different tag from all the other allow Unit X to build Building Y abilities -- it's called the ForceBuildings tag. From reading the Civ 4 modding wiki, the ForceBuildings tag overrides any other restriction on allowing the building to be built by the unit. Also, the +4 culture from Academy never obsoletes, so you can get that bonus after researching Computers, although it isn't really that beneficial by that point.
2. Able to start the Garden of Eden build, without any Paradise Gardens having being completed. I had 10 Gardens being built, even though the requirement was only 7, but it allowed me to begin building the Eden project. Further on this, the number of Paradise gardens is not scaled to map size at all. 7 Gardens for a Gigantic map is nothing.
Paradise Garden doesn't interact with Eden Project at all (although by the names, it probably should, but you can't put a building prerequisite on a Project). Paradise Garden is the prerequisite for the Ascension Gate Wonder. However, there is a problem with the iBuildingClassPrereqModifiers tag for Giant and Gigantic maps. This tag covers the change in the # of buildings required when a prerequisite building is specified. It's 0 for Duel and Tiny maps, 25 for Small, 50 for Standard, 75 for Large, and 100 for Huge; AND has 75 for Giant and Gigantic, which is almost certainly wrong. C2C has 120 for Giant and 140 for Gigantic. That's probably better; I think either 120/140 or 125/150 for Giant/Gigantic would work.
I don't know what to say about your third problem. I know a little Python, but only enough to do a few effects at this point.