I gonna throw my $0. 02 in...
Cut you losses and DON'T let this dealer touch your truck again. Get your $300 or whatever he is offering you and do your research on reputable liner shop in your area.
If you let the dealer take care of the problem, who knows what the repair could look like. If they screwed up once (sub shop), they will screw it up again, only worse. Then you have the whole issue of the pimply teenage punk driving your $45k truck back and forth to the sub shop, not caring about it being a diesel and trying to do burnoffs with it.
Find a shop with the product you want, go talk to them about WHO will do the work (a first timer or someone with lots of experience). Spray in's are definately an art and you want the guy that knows what he is doing.
Finally, ask them how they will repair yours... how do they take the old out? Maybe you don't want to know...
You will never be happy with the dealer and he and the sub shop will make your truck worse.
No one touches my truck unless I personally interview them and let them know the truck is my baby and I'm super anal and they hopefully get that I'm the annoying customer that will "supervise" their every move...
Good luck on a resolution.
Louis