You guys are both awesome; thank you for the help!!! I'll work on this over the next few days and report back with how things go. I'll probably take a picture before putting it back together so you can see what I've done and make sure I didn't mess anything up. Thanks again!

I was wondering if you got this figured out yet? Mind if I ask who you had do it? I think I may have had the same person change mine.

Nope, it's not quite figured out yet. I sent the ECU back to the person who did the upgrade for me along with the wiring instructions. He made changes, sent it back, and I just put it in the car tonight. I tried to fire it up and still nothing. I've attached the current tune and the datalog while cranking. I could smell fuel after I cranked for a bit and I saw RPM on TuneStudio while cranking, but it didn't even sputter. I would appreciate any help I can get. If the tune file looks solid and there's nothing obvious, I can pull apart the ECU and take/post photos of the wiring again.

That spreadsheet is putting a lot of information about upgrading Gen 1 MSPNPs into the hands of shops who really aren't up to the task, unfortunately.

Spark mode needs to be set to 4G63, not toothed wheel. That's the most obvious issue I'm seeing.

What are the issues with toothed wheel? A Miata I am currently working on is set to toothed wheel and running well.

It's the wrong setting if you are using the factory CAS. And the 4G63 mode incorporates the rising and falling edges of the CKP sensor for double the resolution.