Transmission shouldn't have anything to do with it. I'm guessing you have a fuel delivery issue. How's the truck running? Is it nice and smooth at idle? If not, I would clean the MAF sensor and throttle body. Replace the fuel filter.
Don't worry about the truck keeping the starter going. Some years of these trucks (not sure which ones), are programmed to keep cranking until you flick the key all the way to off. My 06 doesn't have it, but I wish it did because sometimes I just let go by habit and it doesn't start.