Obviously the rub mark on the frame rail is unfixable, but it's also extremely minor and doesn't make any noise when touched. The fender liners though, while also not any serious problem, do make annoying noise whenever the wheel is about 3/4ths the way to lock.
First up the forward areas.
Just nail it with the heatgun until the black plastic has a slight wet look to it and then push it in and hold in place until it cools with the heavy gardening gloves I hope you're wearing (light mechanics gloves won't cut it, gets tooooasty). For those tough corners, use a large philips screwdriver to pop the corner in and then continue to hold all the rest with your gloves until it cools off and stays in place.
Now for the rearward one, it's a little more complex, the contact area is much larger and involves the mud flap. Here's the detail of the problem:
Now with the mud flap taken off (4 screws, easy as pie):
Again heat-gun the sucka extensively. Can be kinda hard to get the whole area hot enough and hold it all in at once, and if you try to do it in two parts then the area you've already tweaked starts going back to it's original shape as you heat up the adjacent area =P, but keep at it and it'll work out.
Then I cut out the section of the mud flap that was rubbing, here's the pic of it reinstalled:
And in the end it all worked perfectly, no more rubbing at all that I've been able to hear in a couple test drives so far. Here's what the clearance looks like now:
