I took mine into the dealer and they took pictures of it to send to toyota, i suggest you do the same. The more people that do the more of a case there is that something is wrong.
I do remember there being a gap on mine when installing them, and they went on like you said, one on each side, what i did was wrenched them down tight with my ridgid impact gun. The metal the steps are made of is soft enough that it will bend, just be carful not to strip out the bolts.
Sorry probably a dumb question but, what is a dead pedal and where is it located? Is that a part on the winch, or the truck? Ive never owned or use a winch.