My mazda pickup engine light came on, and the truck is running rough. Almost like its missing a little. It sputters but is still driveable.

Sounds like you have a cylinder misfire. Is check engine light on ?, Have you had the vehicle somewhere to get a code scan? My assumption is that you have an ignition problem that is causing the rough idle and jerk feeling while driving.
Take the vehicle to a shop and have them diagnose the driveability problem that you are having.

I doubt the gasket is the entire problem

Why wouldn't you replace the valve cover
gasket,then explain the driveability ones?

Check the spark plugs for the proper gap (0.044 in) and if the ignition wires are old they might need to be replaced.

i think that when you change the coils you crossed the ignition wires make sure the firing order is right

probable a coil take it to autozone an they will put on a test an tell with one for free

check pvc and check for air leaks around intake and carb gasket use a little carb cleaner if engine sputters while spraying u have a leak

i would first change the fuel filter with it being run low in fuel it may have picked up some trash off the bottom of the tank so change the fuel filter and see if it runs better

check for a lose spark plug lead or cracked elecrod insulation on spark plug

Do you have a check engine light on? What codes?

valve bent or valve seats worn