Ok so this game has been great great fun.
I read that it is really badly bugged so I tried the modpack.

I guess the modpack has been updated over and over so it still has bugs, because the game had/has so many bugs.

I did the assassination quest and told the girl I would take care of him for her....
She said ok and then her and the pirates went outside so I could kill Skole.

Problem is her and the pirates never came back. None of them. I still havent done their quests and I just feel robbed.

Now it seems either I have to just skip all that content or go back and repeat a bunch of content to get to it. I am a bit tired and have a stock of savegames that I backed up to try and see where I can start off from, but I hate repeating content.

Anyone know of what this bug is or how to workaround it with current save game (get the pirates to come back!)?

I know which quest you are talking about. I've done the quest too, and they never come back. I had the impression that when she said they were leaving, it was for good. So I'm not sure it was a bug like you say and I'm not sure there were any more quests to be had from them. Of course you may want to check this forum to be sure: http://www.co8.org/forum/ Though I, myself, haven't been on it. Hopefully they can answer your questions more thoroughly.