Now FWE has an alternative start up option, which I used. I chose to be an escaped slave, which incidentally has a perma-item equipped (a slave collar).
I can't get the slave collar removed via the console and I haven't been able to get the quests that follow Scientific Pursuits and Tranquility Lane to start properly (scripts that aren't running after completion, or something). So basically as far as the MQ goes, I'm stuck. :/
I'm hoping someone who has a lot of experience with either FWE or the console can help me out with this issue and potentially with any other DLC that try to strip the player of their items. (May cause further crashing)