Crank no start, the Anti-theft is engaged but we cannot get through the data link connector?

Sorry, I know that's a lot and half information. If you need voltage readings for anything, let me know. Last thing, I'm not getting a 5-volt reference. Just 0.01 or 0.02. Don't know if that helps with your diagnoses.

From everything you have said it sounds like the PCM is out. I would check the PCM grounds and if they are okay, swap out the PCM with a rebuilt or used unit. Here is a guide to help you check the wiring and the PCM wiring diagrams with ground locations as well in the images below.

https://www.2carpros.com/articles/how-to-check-wiring

Here is how to change out the PCM as well. Check out the images (below). Let us know what happens and please upload pictures or videos of the problem.

***Sorry been super busy with work

I bought a second PCM, BCM, key transponder, gauge cluster and the dash harness, still no luck. Anti Theft won't turn off. I've had a professional programmer/ Locksmith (mobile mechanic who was certified, not very professional though) He couldn't get his $7k computer to read the PCM via Data link connector. We can manually turn it off but when you go to crank it, it turns back on immediately. However, I did find out through talking with other Mustang enthusiasts, a 03 GT/Cobra Dash Harness will not work with the 04 3.9L model. So, I'm going to repair the old harness and re-install it today.
How would I test the Key Transponder on its own? on the wiring harnesses BCM and PCM. Which wires do I probe to test them? Did I mention I have zero voltage to the turn off switch?
Last question, do you know where all the grounds are located and or what should be grounded to the body? (I know everything positive has to have a ground, that's not what I'm asking. Lol) The main ones like starter, engine ground, the battery and grounds that are around it. Forums keep mentioning one by the radiator? Where would or should that ground be?

No problem,

Here are the ground locations, also I have included the data link connector wiring so you can check that out as well. Check fuse #31 in the interior fuse panel. Check out the images (below). Please let us know what you find.

Thank you! I'll keep you updated on the progress today.

please do!