03 Lincoln LS Transmission/ PCM Issue after Sending to SIA

Unfortunately getting to the part of the wiring harness that connects to the tranny is very difficult. I have thought about swapping out the harness but the guy at the tranny shop said if it were the wiring harness the car would have threw a code immediately. It took a while for my codes to come. Not entirely sure what you mean by verify the pcm to the 03 but I did have the PCM programmed to the car and keys. I also ensured that the part # matched up with the stock one.
 
The part matching from the oem unit was the suggection, which you did. I use crc connector cleaner because of Houston humidity every time when reconnecting. I haven't had any issues with connectors. I found DeoxiT as an excellent cleaner as it does a good job then just cleaning also protecting. I've put three rebuilt transmissions in my 04 Sport with 492k miles. I have a 06 Base that i was replacing the pan oil from bottom 1/8npt plug every 500 or so miles the shifting improved. Doing in conjuction adding a dip stick tube port & AN fitting for kidney loop filter pump unit (not installed yet). After the third pan fluid repacement the tranny operation was very smooth. And during four to fifth pan drops (a few screw ups) the observation of oil color seem to get dark quickly. I place a tranny dual oil coolor on the lower bumper but retain the stock cooler for forced air flow when the AC is on. One other observation is the ss fluid line with non-mandrel bend crimps are believed to restrict fluid flow. I've sourced 5/8" id hose with 3/4-16 O-ring boss (5/8" id) barbed fitting to tranny case ports to replace the stock lines soon. Check this article out. Its the basis why for all this work.
Tranny Filter Tech

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