It's been covered a lot previously, but the cost of diesel versus gas is a wash in the scheme of things. You pay more up front but you get all if not more back when you sell it. Or if you do payments you are going to pay a little more a month but again you'll get the difference back when you sell or trade. Operating costs are a little lower with the diesel but the difference is pretty minimal in light of the total cost of ownership that goes along with an HD truck.
I guess the only scenario where I see gas making more sense is if you're really stretching yourself on the purchase price on the front end, which would make the gas up front cost more palatable. Although there's probably a good argument to be made that if you're stretching yourself to the degree that you can't cover the $6500 extra for the CTD vs 6.4 Hemi, you probably ought to be looking at used vehicles anyway.
As far as price negotiations go, just keep it simple. Work dealers off one another on quotes up front, and when you go into the dealership your only points of discussion should be purchase price, financing (having already talked to your own credit union as a backup), any fees/costs they want to tack on and trade value (if applicable). Do not under any circumstances discuss monthly payments because it's way too easy for the dealer to hide the ball if you go down that road.