My experience with flexible body panels like these is if you don't add a flex agent to the paint you are going to stand a decent chance of cracking or peeling of the paint.
Just something to think about before you put too much effort into it.
On a related note, if you remove the panels (which is the right way to do it) pick up the clips, rivets and rubber trim seal from Toyota before you start. The rivets (especially the ones on the quarter panel flare) are a little different than you run of the mill rivet. They are a multi flange rivet that has like four serrations in the shaft. I did not have real good luck with standard aluminum rivets.
Another note, the trim seal on the rear door panel originally had adhesive on the door side as well as the flare side. I just replaced mine and that is no longer true. You will have to clean up the remnants from the factory seal with adhesive remover.
And lastly, you can get the little clear bra piece that goes on the door flare from Toyota too. I got all my parts through my paint guy at cost so I'm not sure what it would cost if you went to a Toyota dealer off the street.
Good luck!