Just a few semi-random ideas I had:
1. Since the first release had so many buildable buildings that forced you to scroll through all of them to find the one you want, it would take a while to go through each one individually and change the tech needed for each to none, why not just perform a mass-deletion of all of them and only add new ones back into the file (taken from a backup file which still had all of them) when needed, since the majority of units and buildings likely won't be in the actual modmod. This would also decrease the download time, since we wouldn't have to download all the unneeded data that we currently do.
2. Would it be somehow possible to have a program that translated NetHack maps into Civ IV scenarios? This would allow for the use of an already functioning map generator to at least give the basic layout of the maps, so that the game would only need to add units and treasures and other features. I doubt it's possible, but it would be cool.
3. For a scenario: you were sent into the vast caverns to explore them and send resources back up to your parent civilization (which would be whomever you choose at the start of the game). The more you send them, the more support you get, and you also can aid them in their wars raging above the surface. If your civ is faltering, you may experience raids into the caverns by their attackers, but if they are winning then they may send some of their more experienced soldiers down to aid in your exploring. Most of the interactions could be through events, but it would be cool if you could somehow ask for extra supplies now and then without having to wait for an event that might give you some.