Running poorly

2002 F-150, 4x4, 5.4 triton 88,000 miles. I had a new motor put in about 3000 miles ago. The other day after I got gas the check engine light came on but I did not notice any problems. Yesterday I was at about 1/4 of a tank and the truck ideled rough until it had warmed up for about five minutes and then ran fine. On the way home from work it was running fime until I started up a hill and the transmission downshifted and them the truck lost power and missfired. The truck ran fine after that until another hill and the same thing happened. When I got into town I filled up thinking it was just bad gas, but on the way to work it happened again. The fuel pump and filter were replaced when the motor was put in. What could be the problem. I live in a remote area and there are not very many mechanics around.