I'll start by saying that your antenna line should NEVER be routed close to your ECU; the EMI from your coax when you key the mic makes it go batschidt. This note is also in the FSM. Science in action!

Have you tried pulling codes yet? The ECU can store them, and not necessarily flag your check engine light. Check that first.

Might also check your 02 sensor harness to make sure it's okay.
When's the last time it was changed, or a thorough tuneup done for that matter?

Couple other things; has the t'body been cleaned lately (see the maintenance article here; for a V6, but same idea)
TPS behaving/set up correctly?
Spark plug wires-- how old? That would also point you to the coil/ignitor
Distributor cap/rotor

You say variable stutter; if the EGR valve was carboned up, that usually is around 2400 rpm or so.

Anyone else?