Truck idles a little rough when at red lights out stop signs.. Doesn't do it after while.. Check engine light is on.. Also the truck beeps when I first crank it up and does same beep little while later after driving.. It's a2003 4.2 man trans

 

The beep can be a secondary warning for a few things. If it beeps after start up multiple times, that is usually an indicator that your SRS system is not activated and the light on the cluster for it has burned out.

Does the air bag light come on when the key is turned on?