check engine and repair airbag lights on

After changing my alternator and battery,my check engine light and airbag light stays on and the headlights,dash lights flicker,now my truck is idling rough and the whole truck will shake,it doesn't do all the time,does it hot or cold,while driving it still runs great and hasn't lose power.the truck is a 2004 ext cab chevy silverado z71 with the 5.3 engine and a whipple supercharger,I also just changed plugs and wires,what could be causing the problems,thanks