For the rogue stars, just open the GalaxySenarioDef file and remove all reference of them from that file (remember to update the counts at the start of each section). If the super pirate base has a different entity from the regular pirate base, doing the same thing with them in that file should correct that problem. If they just modded the normal pirate base and kept the same name, just deleting the file from the mod should return the normal pirate bases.

Okay, when you open that file scroll down until you see something like this. (Rogue starts are considered by the game as planets right? It's been a while sense I've played a mod with them)

planetTypeCount 45
planetType
    designName "WeightedNonIce"
    designStringId "IDSGalaxyScenarioTypePlanetWeightedNonIce"
    orbitBodyTypeCount 37
    orbitBodyType "Terran"
    orbitBodyType "Terran"
    orbitBodyType "Ocean"

...

The count that's probably causing you problems is the orbitBodyTypeCount. This is simply a count of all the orbitBodyType lines in a planetType section. So whenever a planetType mentions a rouge star, just delete that orbitBodyType line and then reduce the orbitBodyTypeCount for that planetType by one. If a planetType references only a rouge star and nothing else, it is probably okay to leave it (as that shouldn't be part of the map generator). However, if you choose to delete the entire planetType section you have to reduce the planetTypeCount by 1 as well.

Another cause of the problem could be related to the super pirate base, but I need to know if they have a seperate entity file for it or not.

Alright, for the pirate base you're going to want to make sure you have something looking like this in you GalaxySenarioDef file.

planetType
    designName "PirateBase"
    designStringId "IDSGalaxyScenarioTypePlanetPirateBase"
    orbitBodyTypeCount 1
    orbitBodyType "PirateBase"   

This should prevent super pirate bases from spawning if they didn't modify any of the map files. If you don't have this then it could cause the map to dumb because most maps expect a "PirateBase" planetType. If you're still having trouble, upload the original 7ds GalaxySenarioDef file and I'll do it for you.

Check to see if they are still in your recycle bin. Otherwise, just reinstall the mod.