Well, I don't have to change the intake or thermostat! I got the wiring manual a couple weeks ago. Couldn't find the under hood to under dash connector in it. Thought maybe I had a very early 2003 with a 2002 connector and it changed, or a very late 2003 with a (changed) 2004 connector. So I did what I should have done before ordering the wiring manual -- I checked the VIN. Turns out it's a 2006!! A lot of the wiring is the same or close enough, but I'll probably put the 2003 wiring manual up for sale on FB Marketplace or e-bay. Unless someone here needs it -- I'll take a $10 loss, $35 and I'll pay shipping.
I also contacted Mars. After getting a pinout of the under dash connector I'm sure I could have sorted the wiring harness. It would have taken some work, and I think I'd ditch the factory fuse and relay center since I'd be deleting half of it. So re-wiring up the relays. I still had to send the ECM in for re-programming -- more so since it's a 2006. That was going to be $400 no matter what. Mars stand-alones 2.3L Eco-Boost harnesses for $650, so $250 for them to fix the harness and they include a compact relay/fuse center. I called to make sure they would do a non-boosted engine, and they now have my harness (sent about 10 days ago). Said it was possible it might cost a little more, but I doubt it. Has to be easier without the turbo, but then it is different and that might take some more time. Hoping it won't be more than $100 more, but I'm committed now!