When you say "alot of the factions dont have their units", I presume you are talking about custom battles. You need to switch the single player files (meant for the campaign) with the multiplayer files (meant for multiplayer and custom battles). As the Trivial Script does not work for you, you will have to do this manually. You will find the files under [your/path/to/RTW]/EB/mp game edu backup. For each of the three files, find their equivalent under EB/data, then copy them into this location.

When you want to play a campaign after doing so, you will have to do the same procedure, but this time with the files under sp game edu backup.