Hmm those are some interesting bugs you've found, @Prof. Garfield may have some advice but otherwise we may have to wait until if/when TNO comes back to the site and works on a new version of ToTPP.
I have vague memories of someone reporting that they stop getting the foreign civ wonder messages. I can write Lua code to compensate for that. I haven't heard of civs stopping research. However, back when I was playing standard Civ II games, it was pretty common for some tribes to fall behind in research. Have they actually set their science rate to 0, or are they just falling behind?
Are you playing a game with 7 players? If not, then the missing "Key Civ" will raise tech costs for some tribes (since their key civ has 0 techs), and they might not be able to compensate for the deficit.
There is a mechanism in the game called the KeyCiv that tries to adjust a player's beaker costs as the gap in techs between players grows larger. A brilliant player called Samson discovered that your KeyCiv is based on cross-referencing your PowerRating with the colors of the Player List.
Here are the two lists:
So if your PowerRating is Mighty (see top line of F3), your KeyCiv is whatever player is Orange. If that is not you, your beaker "cost" for the current research will be adjusted by a factor based on the difference in number of techs each of you has acquired since the beginning (starting techs don't count). If you have less than your KeyCiv your beaker cost will be lowered somewhat. If you have more, it will increase. Each "jump" in cost happens for every three techs difference, so you don't have to worry every time you get a tech, just every three.
1. Duplicate the Test of Time\Original folder, so you can easily revert to the 'true' version if necessary.
2. Extract this file into your Test of Time\Original folder.
3. Make sure that in the TOTPP launcher, you have enabled Lua scripting and Lua events (these are disabled by default when you set up the patch).
4. Start an original game, and enable the Lua events when you receive the warning.
You should be able to play the game, and these Lua events will compensate pretty closely for the messages you are supposed to get. The messages I wrote have the title "Travellers Report*" instead of "Travellers Report" (note the *), so you can tell the difference between Lua driven messages and "genuine" messages, in case it matters.
I've only briefly tested this code. I played an OCC game to about 550 BC, just enough to see a few wonders started, changed, and completed. Let me know if you run into problems. As a bonus, I also added the ability to press SHIFT+F1 to enable the One City Challenge rules. Basically, it just prevents huts from giving you advanced tribes.
Bug report: ToT isn't notifying me when another tribe starts a wonder. I'm enabling Edit control + No CD + Save file extensions/Extra unit types. If I only enable Edit control + No CD I do get the notifications, so extra unit types seems the cause. I'm uploading a savegame and my config just in case.
Building on this, it seems different save extension options interfere with different wonder popups in Game.txt: as stated, 'Extra units types' blocks @STARTWONDER and @SWITCHWONDER, and 'Extra technologies' blocks @ALMOSTWONDER.
A request: The mod loader can parse the special rules for the Fantasy and Sci-Fi game modes; can support be added for Extended Original? The flag that prevents the spaceship arrival from tallying the score seems to be hard-coded.