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I tried using the connectors under the dash but it still had numerous codes stored.

I then disconnected the battery for a while and here is what happens -
Reconnect battery terminal (key is not in ignition)
Connect the connector under dash to flash codes
Turn key to ON but not started

It will then flash every code that is for an out of range voltage ON EVERY ITEM. Meaning all four injectors, the knock sensor, the maf etc... I could get a specific list if it helps.

The odd thing is that when the car is running the check engine light never comes on and its running perfectly otherwise so I am confused how it can have all of these instant codes.

After you've started and run the car for a while, do you have those same codes stored?

Have you tried clearing the codes using both the green & black connectors?

Have you tried running the d-check mode using the green connectors? If so, what codes, if any come up?

I've run across and others have run across codes that won't clear using the battery method and have to use the green & black connectors. My only way out there guess is that it may have something to do with the california jurisdiction pin on the ECU. Do you know if your car is a california jurisdictional car?

I have tried various methods BUT for completeness I am going to try each of your suggestions now. Yes after running the car for a while I have the same codes stored.

According to the emissions sticker it is a California car. If this can't do it I'm going to cut that California wire.

To clear it with both black and green connected do I have to do the throttle thing with the car off and drive in fourth gear for a few minutes while at operating temperature?

CODES CLEARED
I waited for the fans to run, turned off car, connected both connectors then followed the steps here http://legacycentral.org/library/literature/codes.htm
When I first started it was flashing 6 6 6 and once I started driving the light flashed exactly once every second.

Damn I just realized these codes have probably been stored in the computer for the 13 years (the last time it visited the dealer). I kid you not it had stored codes 13-17 22-24 32, 35 and 3-4 more that I didn't write down because it was a ridiculous list.

Does the California pin do this? The strange thing is that my 91 LSi was California spec and didn't have super memory.

You know I really don't know what triggers the super memory, but there have been other board members that only could clear the codes using the green & black diagnostic connectors. Disconnecting the battery did not work.

The california jurisdiction is just a guess, but it'd be interesting to see if those that did have similar issues also had california jurisdictional cars.

Hmm, i should check that out. Ive tried and tried to clear codes on my ecu and they wont clear. Ive even used revscan to clear the memory but i'll still have the same codes stored.

Yeah, give it a shot.

I'm assuming it's the "Jurisdiction ID B56.11" pin?

Yes, that's the federal/california pin.

Well, then im going to cut that wire assuming it's there and try to reset my ecu with revscan and see if that clears all the memory.

or connect both and drive it if that doesn't work...

Ok here's the results. The wire is there on my harness, which would mean my harness (not car) is cali spec. B56.11 on my harness is green/black stripe (or some dark colored stripe, it's hard to tell when you're under the dash.)

I disconnected the battery and pulled the B56 plug off the ecu
I cut the wire (crimped on 2 insulated connectors in case the wire had to be reconnected i.e. didn't work.)
I reconnected the battery, connected my laptop to my ecu with the evoscan cable and reset the memory, this didn't clear stored codes.
I put kiddo in his car seat, connected both black and green connectors and went for a little cruise around the block.
After i got back i connected the black connector and turned the ignition on and VOILA NO STORED CODES

By the way, in case some of you haven't thought of this, I have 2 toggle switches just next to the storage tray on the left side of your steering wheel. There's leads of wires coming off those going to my green and black connectors at the ecu. It's a million times more convenient then having to get under the dash and connect the plugs while trying to work around the wiring harness. Even worse if you have car alarm wiring all over the place under there...

Glad the codes cleared, but I'm curious, did you try the green & black connector method previously without any success?

There have been numerous times when i have tried that and it pissed me off because i could never get the codes to clear. Which makes me wonder if cali spec cars had to have some sort of special software to actually clear the codes.

Ciper cleared his with the green & black connectors.