Probably the APPS. If you know someone with a 1998. 5 to 2002 truck with the same style transmission (manual or auto) and his truck doesn't have symptoms swap his APPS into your truck and see what happens. No symptoms means replace the APPS. PM timbo here on TDR for a less expensive better quality aftermarket APPS.
If you don't know someone with a similar truck just go ahead and buy the new APPS from timbo, if you don't need it now you will later.
Godspeed,
Trent