I forgot to mention it, but the twined wires are to allow me to connect and enable sequential ignition. I need to do some research before heading down that road.
Reverant answered my query about the CEL. I had to connect to TunerStudio, open a new project and let the program detect the new firmware. TS didn't have the necessary updates to operate with the new firmware so that was downloaded. Once I had everything done I fired her up, and all was good. I drove to our local cars & coffee, there were quite a few folks there from the Facebook Miata group I am on so that was fun. Wasn't able to wash her beforehand due to temperature (I have no problem washing a car when it's cold out, but not that cold).
Got her washed that morning and took a drive on one of my favorite backroads this afternoon. Should be some good days during the week to permit me to do some tuning.