There is no question here. Take the damn thing back and make them fix it on their dime! There is no reason your truck should be in any shop sitting for 5 weeks, there is just no excuse for that. I don't care if they were completely replacing the motor, 5 weeks is rediculous.
If they refuse to fix the problem then leave the damn thing there and tell them to give you your money back. This is why Ford has a bad rep because they have no quality control over their TECHS, some are good yes, but most are junk there to collect a pay check and just limp these things along until they are out of warranty.
Also you said you just bought the truck and that it was messed up upon purchase. If you bought the truck from them you should have made sure everything was up to specs before you drove off the lot, just my .02.