I can't offer a fix to the terrain incompat issue... couldn't even figure out how to repair it for my OWN savegame (so its a bit annoying that I couldn't completely check my own fixes here against my current saved game.)
Anyhow, I've just updated the SVN with the following:
1) Fixed Divine Prophet ai issues with how to handle prophets (which religion to found and when to found it.) They shouldn't be stuck on holding more than one prophet (a rare Limited Religions scenario anyhow) anymore.
2) Fixed Divine Prophet Can Spread issues. Repaired the break in my coding that was allowing any religion to be founded at any time by a prophet when Choose Religions was NOT on.
3) Fixed All Divine Prophet/Limited Religions/Choose Religions compatibility and bug issues.
4) Repaired Limited Religions without Divine Prophets, both with and without Choose Religions on. (no more pesky games getting stuck due to repeating religion selection popup!)
5) Repaired fix to Nukefix as per Koshling's instructions, which opened up a lot more compatible modding understanding (thanks Koshling!) - note... not fully tested yet so COULD have a bug somewhere... we shall see once the SVN can get back to full savegame compat.
NOTE: PY modders should know that ANY and all referrences in Python to CyGame::isNukesValid should be changed to CyPlayer::isNukesValid. There may be impending errors until these are rectified.
6) Added a tag to unitclassinfos and propagated the capacity for that tag to be utilized in many of the modules. Tag is bUnlimitedException and it can be used (just after the National Unit limit tag) in UnitClassInfos to cause this particular unit to ignore the Unlimited National Units option and remain limited. Thus, for some units that are critical to limit such as farmers, tribes, bands, 007, etc, you can put <bUnlimitedException>1</bUnlimitedException> just after the National Unit limit tag and it will retain its limitation.
7) Fixed the Unlimited National Unit unit count display on the Unit Help mouseover. Now, when Unlimited National Units is ON it will only keep track of how many you have left to build if the national unit has been given the Unlimited Exception. It won't show or indicate any limit on all other units that are normally National Units.
I think that's all for this update.