Unfortunately, this has hit a dead end numerous times. Here is an outfit in Houston that didn't have any luck with the ECU:
“UPDATE.
I just got back from Houston. First off my 03 protege5 is running a 5MGA eec-V. Ya'll might want to compare that to ya'lls. It appears that the service port was disabled at the factory. One it was coated with that varnish looking stuff. We scraped that off but the Tweecer wasn't able to talk to the PCM. the PCM noticed something trying to connect but otherwise was unable to talk to the tweecer. Apparantly the Ford PCM has some jumpers to enable or disable the service port, but it looked like mazda had removed the jumper posts. Since we didn't have a schematic of the pcm board and his partner in Dallas has all his diagnotic tools we weren't able to figure out where the jumpers should be to put some in. So currently it's a no go. However he said he is going to locate and purchase a mazda protege ecu and play with it. Said he'd let me know what he finds out, but the marketability isn't really there since most people don't want to have to modify they pcm. But he seemed to enjoy the challenge so who knows. Sorry guys. BTW the Ford PCM is rather complex LOTS of different tables. Several different base tables for both fuel and ignition. Then there are multiplier tables that modify the base tables for various conditions. It can be rather confusing for anyone not thoroughly experienced in tuning ecu's/pcm's. As of this point I guess I'm going to be using Unichip to modify the output data, unless at somepoint down the line tweecer can be made to work with my pcm. Oh, before you ask. Mazda flashes/updates PCM via the OBD2 port, which is located on the drivers side and accesses the pcm via the huge wiring harness.”
Tweecer response 6 years later: "Ahhh, now it comes flooding back. I do remember a hot afternoon of trying to get his EEC to communicate with the TwEECer. I did try (not real hard) to find an EEC, but only came across two locally which one guy wanted way too much for and the other did not work. So, basically just never got anything to work with and was not really interested in putting out much effort for such a small market.
If someone can get a unit for under $100, we can take a look at getting the jumpers figured out. It is possible that not ALL PCM's have the J3 port disabled. I may be able to read the calibration from the OBDII port, allowing me to hack n crack on the strategy while we wait to get a unit to test with."
For what its worth, a Houston tuner saw my ECU and claimed it was strikingly similar to either the ford focus or ford probe ecu (I do not remember which one). However, whichever one it did resemble, he had full control and the ability to flash it. He suggested to swap a couple of the pins that didnt line up, and replace the stock protege ecu with the one that he had. Apparently the connector was the same as well, just a few pins were different. I did not follow up.