It might be useful for you to start over and play in a style that makes best use of the changes Medmod offers. There is a file that details what provinces each faction can build troops in and it is imperative to capture and hold these provinces early in the game so that you can start building them up to produce top level troops in as many provinces as possible. Most factions get about 9 provinces to build troops in, although there are a couple (like Malta) that let you build crusader type troops as any faction. If you plan this way you can usually have enough of an army to counter other large factions. And a Medmod game usually ends up with 2 or 3 other large factions to make the end game more interesting. I am not sure what Wes and his crew did, but factions seem less prone to rebellion in Medmod and that is a good thing.

Personnally, I think Medmod is the best mod out there if what you want is a tougher game. Try playing as the HRE in any era for the ultimate challenge.

GL, HF.