Your setup should be OK. It shouldn't cause any bugs and I think you gotn't any error messages related to any *.txt file.
One problem could be that you used the scenario file structure for your mod. I know you have to put the map itsself into a scenario folder but that should be everything.
I tried it too and I got the various savegame bugs, like the extra turn bug if you reload a savegame or corupted savegames. I played my private mod that includes DiploMod and at ones most of my savegames where corupted also savegames that I already loaded successfully.
I had to start a new game.
Therefore for your next game you should use ModSwapper take a look on CityMod2 that is available on my page for reference. If you have some questions about ModSwapper please ask.
For your current game: I have no better sollution as you found you can deal with this bug ( I know it is a poor or no real solution for your current game), but you can bring your game to an end.
-Martin
By the way one minute is nothing
for a turn in Civ2 I needed one and a half hour just for one turn with everything (moving 200 settlers
, city improvements in 200 cities on a 486er and I thing my last turn on my K6 233Mhz with 64Ram needed longer and that was only the normal setting on the biggest map of Activision. But my new comp is now a little bit faster....