I don't know if you kept posting because not enough people responded or you just weren't sure what you were doing, but if noone is responding to a thread, just bump it up to the top. If still nothing, we don't know the answer. If you're going to be posting a lot, search for the answer first before you start a thread. I had nerf bars on my '02 before I realized that they were useless. I didn't have to remove the mudflaps, however they came off anyway after I tore them off backing up over a large rock. See if the manufacterer has a tech line on their website. They could probably give you some tips.
2001 Tacoma, slightly modified