FWIW, I just put a Cardone PCM in my 98 ZJ last month. The one that was in there was actually a Cardone PCM (don't know how old - I recently bought the ZJ). Anyways, I was nervous about swapping it out (even though I was replacing a known bad one) but the Jeep fired up and ran great.
And I didn't know it, but my ZJ was a California emissions Jeep (so I had to make sure I got the right PCM).
The instructions for the warranty said I had to have the VIN uploaded (flashed) into the PCM. So I brought it to the local Jeep dealer, and they told me they had to do it with the PCM in the vehicle, and they had to pull the equipment out of storage to do so (since it was "so old"). The dealer told me at the same time they would upload any updates that have occured since 1998. And it would take a couple of hours. Fine; I dropped it off the night before.
Well the next day and $120 later I picked it up, and they said the Cardone part already had any and all updates already installed. The odometer was correct too.
I got mine at O'Reillys - a Cardone part. In reading before I bought it, that was the recommended brand to get. It wasn't cheap, but it's not worth trying to save a few bucks if it leaves you stranded somewhere.