mudguards are integrated in to the fender flares. There would be a hole if the mudguards were removed.
The very rearmost stock fender flares are to be removed. I can't remember if it's just the one on the gas cap side, or both rearmost ones.... I'm pretty sure it's mentioned earlier in this thread.
I am not aware of any TRD sliders. There are a couple different models of running boards though.... can you post a pic? I had to notch my front bushwacker flares for my OPOR sliders. It was easy, and I cleaner job than the pic a couple posts up.

(sorry 3wbdriver.... I really appreciate your input on them and I used your idea. I had to tease)