truck is running like crap!!

[thisolechevy]

Hey guys I am in need of dire help!! I was getting my truck ready to drive home from the body shop (whoo-hoo, finally after 2 months) and when the body man moved my truck from the lot into the bay to finish it it cranked right up and sounded great!! then we let it run for a while and shut it off. I had him shave the fuel tank from the cab and I installed a new fuel cell in the bed when the truck was running great this morning I had just run some 5/16" fuel line into the bed and into the filler neck on the old cab-tank. Then I finished installing the fuel cell and plumbed the lines, I then proceeded to pour about 2-gallons of fuel into the fuel cell. After this I poured more fressh fuel into the cell, and cranked the truck and let it run for a couple of minutes. I forgot that I had never connected one of the fuel lines (stupid me) and the truck sputterd to a stop, I connected the lines and now it wont run good at all!!! I checked all lines for kinks and such, cleaned my fuel filter, made sure there was good gas now what? I need help quick