There is so much in that post, Timbatim! Are you familiar with the preferences script called simply "bumcheekascend"? If you look in your browser window you should see a pull-down menu over to the right, at the top, that says "run script". Choose bumcheekascend, and there are a few dozen preferences you can select. One of those being "bcasc_ROFL Set to true if you want to do the Baron's quest even though it is no longer a required quest". Flip that switch to "false" and that's half your problem solved. The other half is your CCS, probably. Make sure that auto-attack is not set (or that it is set to CCS, and that you don't have the adding machine targeted for assassination in there somewhere). You might want to check your choice settings within mafia as well, I find some of them will bend nicely to the will of BCA, while others just don't, for whatever reason.
Leveling, bca preference - level with clovers, without, don't/use temple to level...there are a few settings for that too. Sometimes bca will want to level when all you need is hair spray or a change of gear. It's not perfect, but it sure is a damned sight better than trying to all this manually!
You should check your auto-recovery settings, or alternatively, maybe check out Bale's Universal Recovery script. I'm sure someone will be along shortly with more/better info, and possibly a link.
For the familiars you'd have to go into the data file, find the relevant familiar lists, and do a little editing. You can also choose your main familiar in the relay browser script thingitz I mentioned above (I know, I'm *so* damned technical).
Good luck in your run!