Today my buddy came back over and brought his diagnostics tool to check out the car. I mostly just stood by and turned the key over when I needed to and stuff like that while he worked. The following is what he told me to put on here for you guys to ponder over:
1) He set the total timing with SPOUT connected to 32* 'just to be safe' he says
2) The diagnostics tool he brought (Snap-On) would not communicate with the computer after it was hooked up and information was entered into it. Yes, before anyone asks he is competent and knows how to use it.
3) After the car finally reached operating temperature, the coolant temp sensor showed 2.9 ohms resistance. That reading was from the two leads inside the connector on the sensor as you said above. (I'm assuming he had the meter on the right setting when he checked it)
4) It took a while to get the car to warm up due mostly to the electric fan running constantly.
He said he would talk to a guy he used to build engines for who works only on fuel injected Mustangs and see if he also has any insight to what may be going on. But more than likely when I'm off work Friday I'll spend the day loading it up and hauling it to a shop.