F150 mechanical help needed.

Ran battery dead today working on trailer lights like an idiot. Hooked battery charger up and It blew some fuses. Fixed all of them I think. Ran truck to let battery charged. Noticed it was blowing a little black smoke but then it stopped. Check engine light was on and the wrench symbol. Un hooked battery to reset it. Check engine light went off but wrench stayed. Truck is missing bad. Pegging out at 4200 rpm and spitting and sputtering bad. What do I need to do? 2004 5.4 liter 170,800 miles on it. Only thing besides normal maintance is I changed some coil packs