Another option ,if you feel like your rep is too messed up, is to recreate the ship and to transfer the equipment via a friend in Connecticut (if the equipment is worth it). I found in the past that this is usually the faster and more convenient way of dealing with such rep problems rather than trying to grind it back to a "better" state. It's at least always an option to consider imo.
I guess this may be helpful for you to find out, if you want to grind up some reps and which are actually possible for you to grind up and which are "locked" due to being rephacked.