I put the stock injectors back in and got the car running on the oem ecu. With the car running and warmed up the tachometer gauges and fuel injector gauges have no readings. I am getting readings from AIT, coolant temp, and the o2 sensor.

Man this isn't going to be a setting in MS that we can help you with, sounds like you've got a pretty good deal of wiring problems so far.
Any luck reaching Adam?

Yup, until you get a tach signal to the MS, you are wasting your time.

Go through the instructions here http://www.diyautotune.com/tech_arti...azda_miata.htm

Go down to near the end of the article and look at the two pictures of megatune settings with "Power Cycle after Changes" at the top of em and make sure your settings are the same, then try again to get an RPM signal. Also I would swap back to the stockers if it was me, though it is a bit of a hassle to do so.

I have swapped back to the stockers until everything gets figured out with the ms. I've gotten pretty good at taking out the fuel rail now that I've done it 3 or 4 times.

All this will have to wait as some other problems with the car have arose.

make sure you buy some new o-rings and keep them handy... also, make sure you check very closely for leaks everytime you swap them out. It sucks seeing to see cars this nice burn to the ground.

Do you have d1 and d2 jumpered on your board? I didnt have d2 jumpered and wouldnt get a rpm signal because of that. Actually can you open ur MS and take a pic of it? I will compare it to mine to see if I notice anything diffrent.