Misfire is a solvable problem, you are definitely in better shape than what it sounded like at the beginning of the thread.
Have you had a chance to open up and inspect the engine wiring harness where is passes the EGR pipe? That's a common location for wiring shorts (search the forum and you'll find plenty of info).
Personally I'd make a plan to pull the upper intake (not that hard) and address the following (all are either PM or will help with drivability):
- Wiring harness inspection/repair and secure it away from the EGR
- PHH (pesky heater hose) and throttle body coolant hoses
- Fuel filter (these are often neglected)
- All vacuum hoses under the intake
- Pull all of the injectors and send them in for testing and cleaning, install with new O rings
- Valve cover gasket and spark plug tube seals
- Upper intake gaskets and throttle body gasket
- PCV valve and ventilation hoses
- Intake hose
- Spark plugs + wires
- Cap and rotor
- Deep clean throttle body, check and adjust TPS (throttle position sensor) and throttle cables (including kickdown and cruise control)
- Clean out the IAC (idle air control) valve and port, test per FSM
- Air filter
- 02 sensors if they are old
- Once up and running again and codes are gone check ad adjust the base ignition timing
Once you have a plan of attack you can order a bunch of OEM parts from partsouq and have it all ready to go. Sometimes its just better to dive in and knock out all of these together since everything will be much easier with the upper intake removed. In the process you'll take care of the normal tune up items as well as any vacuum leaks which can be difficult to chase down and cause a lot of drivability issues.
Oh and before you take it apart give the engine a good cleaning.
Have you had a chance to open up and inspect the engine wiring harness where is passes the EGR pipe? That's a common location for wiring shorts (search the forum and you'll find plenty of info).
Personally I'd make a plan to pull the upper intake (not that hard) and address the following (all are either PM or will help with drivability):
- Wiring harness inspection/repair and secure it away from the EGR
- PHH (pesky heater hose) and throttle body coolant hoses
- Fuel filter (these are often neglected)
- All vacuum hoses under the intake
- Pull all of the injectors and send them in for testing and cleaning, install with new O rings
- Valve cover gasket and spark plug tube seals
- Upper intake gaskets and throttle body gasket
- PCV valve and ventilation hoses
- Intake hose
- Spark plugs + wires
- Cap and rotor
- Deep clean throttle body, check and adjust TPS (throttle position sensor) and throttle cables (including kickdown and cruise control)
- Clean out the IAC (idle air control) valve and port, test per FSM
- Air filter
- 02 sensors if they are old
- Once up and running again and codes are gone check ad adjust the base ignition timing
Once you have a plan of attack you can order a bunch of OEM parts from partsouq and have it all ready to go. Sometimes its just better to dive in and knock out all of these together since everything will be much easier with the upper intake removed. In the process you'll take care of the normal tune up items as well as any vacuum leaks which can be difficult to chase down and cause a lot of drivability issues.
Oh and before you take it apart give the engine a good cleaning.