Per memory: All PAE games started with the K-Mod dll plugged in were bound to crash after a certain period of time. Scenarios quite immediately but there is nothing to be changed here. As I thought, they bring you closer to the crash because of their complexity at the start, in this case just because many technologies are already acquired by the different Civs.
From running these games with a debug dll, it appeared that the cause of the crash was to be looked for in the buildings, precisely "buildings available to be built" in the pop-up list or in the City screen.
I will spare you the process of trials and errors (xx hours of crashes - I hope that my computer will forgive me!). The problem is actually a combination of the CIV4BuildingInfos.xml and the CIV4CivilizationInfos.xml (which defines the special buildings that are for your Civ only - the UBs - and the buildings that you are not allowed to build).
You may ask: how come it is problematic since a vanilla dll does not crash? I don't have the exact answer. K-Mod has changed so many things, including settings for setting up lists of things so only Karadoc could answer that I guess.
The bottom line is that I found in the BuildingInfos file three cases where a Building A needs an existing Building B to be built, but with a contradiction in the CivilizationInfos file: your Civ may apparently build Building A but is denied the right to build Building B => Crash.
Case 1) Spartans (CIVILIZATION_SPARTANER) can build BUILDINGCLASS_SPECIAL1 - Building Type Acropolis but cannot build a BUILDINGCLASS_SPECIAL6 (in this case Building Type Agora) which is needed in the City as a prerequisite for the Acropolis.
Intended or mistake?
Case 2) Several civilizations are denied the right to have a BUILDINGCLASS_SPECIAL3 (School or Gymnasium) which is a prerequisite for building Academies 1-2-3-4. Maybe this is intended but it crashes the game.
Case 3) Barbarians cannot build Walls which is a prerequisite for High Walls. This does not crash the game, probably because Barbarians are excluded from the process at a certain stage in the coding.
EDIT: or because they don't have the technology yet? Better be safe than sorry and solve that potential conflict as well. They should be prevented from building Babylon Walls as well.
Pie, the solution is simple: since the problematic files are in the SPECIAL Buildings, and that you have fake buildings as a default for the Classes 1 to 9 (buildings not buildable anyway because iCost = -1), the easiest way is to delete all entries in the CivilizationInfos that have a 'NONE' as a Building Type for BUILDINGCLASS_SPECIALx.
I have done that change for the testing: I played the Scenario War of the Diadochis for 20 turns without crash. Here is my file, compare it to yours to see the changes (note that I have assumed that Spartans should be able to build Agora - if not, the Acropolis should be set as unbuildable for them).
For the happy testers who have still a copy of my package, replace this file in the appropriate PAE folder. Let's cross fingers that you can now resume your save games without a crash.
Pie, I'm waiting for your reaction to continue. Still it might not be the end of the problems. Testings should resume and the debugger still throws several errors and conflicts, so far without crashing to desktop.