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1994 2.3l still used ICM(ignition control module), this is a stand alone module and doesn't need the computer to operate spark.
It is connected to the CKP(crank) sensor and to the two coil packs.
CKP sensor tells ICM when to spark #1 and the other cylinders.
In 1995 and up models the ICM was IN the new version Ford Computer not a separate part, just FYI.
The ICM does pass that timing info on to the computer for Fuel Injector timing, and computer does send ICM spark Advance and Retard "suggestions" based on Driver input, i.e. gas pedal position, RPM and Speed.
The ICM only sparks the exhaust side coil pack during startup, starter motor turning engine, intake spark will start when engine is above 400RPM, so after starting.
Ford Coil Packs use Waste Spark system
In your coil packs there are only 2 coils each
Cylinders #1 and #4 share a coil, and #3 and #4 share a coil, on each coil pack.
Each coil pack has 3 wires, 1 will have 12volts when key is on, this powers both coils in the pack
Each of the other 2 wires is used to fire 1 coil in the pack, 1 wire for coil #1/#4 and 1 wire for #2/#3
Using a spark tester can be a bit tough with waste spark since 2 spark plugs are wired in series sharing 1 coil, so one wire can show weaker spark because spark testers are set for normal spark(+ to -) not reverse spark(- to +) .
Both spark plugs in each cylinder fire on both compression stroke and exhaust stroke when engine is running, they do not alternate.
Dual spark plugs was done to lower emissions, engine will operate fine with only 1 spark plug working in each cylinder, i.e. startup.
Codes, found here:
http://www.therangerstation.com/tech_library/3digitcodes.shtml
998 test code, ignore it
543 Fuel pump monitor circuit shows no power
218 IDM signal open or high or left coil pack failure
223 Dual Plug (DPI), SPOUT or IDM circuit fault
224 Failure in ignition coil primary circuit
543, Computer closes Fuel Pump Relay to send power to the fuel pump, computer has a wire connected to fuel pump's 12volt wire that tells computer that the fuel pump relay DID close and fuel pump is getting power, 543 means at some point Fuel Pump lost that 12volts when computer had relay closed.
Now fuel pump relays run about $6 so most just replace that relay to see if that was the problem, it is in the engine fuse box, it could be a wiring issue but replace relay first.
Obviously if fuel pump power is intermittent engine would stall or run poorly with lower fuel pressure.
1994 fuel pressure should be 30-40psi at the fuel rail(injectors)
223 is almost always wiring problem, SPOUT(spark out) is the signal the computer sends to the ICM for spark advance/retard info
218 and 224 can also be wiring issues
Now all these codes can be wiring related, so it might be a good idea to check the computers wiring harness/connector, if some water gets in it can cause problems.
You can also "pop the top" on the computer and have a look at the circuit board.
Here is a look at the 1994 and earlier Ford Computers:
http://www.auto-diagnostics.info/ford_eec_iv