I took lots of pictures (only 8 weeks after we got it) and emailed them to the dealer. They said not to worry, it's 'rail dust' which is quite common on vehicles they get from dust buildup on transport. i.e. it's not part of your truck that's rusting but little flecks of external metal dust that are doing it.... anyhow, put it in for a few hours and they cleaned it very well, no rust and the truck looked cleaner than new. Very happy.
Your problem may be more severe than this, I don't know, but hope this helps.