I have a 2000 TJ with auto and california emissions and was going to order a replacement ECM from a junkyard, but the guy i talked to told me I needed to call a dealership and see if the part needs reprogrammed for my vin number. I called my local dealership and they said it does, but I'm confused because the ECM in my TJ right now is actually out of a Cherokee and it runs fine except that it is always showing the check engine light due to it not detecting the cherokee's electric fan relay(which keeps me from knowing when it is actually throwing a code i need to be concerned about).
As you have found already, the correct part number ECM will run just fine without re-programming. If your state performs emissions testing and they inspect the ECM, the VIN programmed into the ECM will need to match your Jeep.
You can get the ECM re-flashed, but be aware that many Dealerships will refuse to do the job. There are a number of on-line and eBay sellers that will flash your VIN, and the current programming, into an ECM and send it to you.
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I completely swapped my 97 TJ's ECM when I converted it from a manual transmission to an automatic transmission. The subsequent smog test here in California (probably the toughest in the nation) did not detect the different ECM or flag any VIN error.
I did some more research and found out that the 05 and 06 models do need to be vin matched for everything to work correctly, but previous models don't.
Matched to what, exactly? The auto module is contained within the ECM, and I'm not aware of any other computers in the Jeep. Unless there's something in the gauge module, I've never heard of reprogramming those though.
I know 01-04 came with a variety of ECM's due to engine and mapping changes. I think 97-00 are more or less the same, but don't take my word on that.