The swap was a success and I just thought I might put up a little info to help out anyone else who might be tackling this job.
Miata Community Wiki | Automatic To Manual Conversion
The above link is useful pretty much for the wiring. It has a couple pictures and description of the wire colors you need to connect to the neutral safety switch and the reverse switch.
There is a ton of stuff this guy wants you to do that is unnecessary. There is NO NEED to pull the engine to pull the auto trans. You DO NOT need to pull the dash to change the pedals. I still don't get why this guy wants you to take the seats out either.
There is a ton of people saying you need to swap over the wiring harnesses and ECUs. False. I suppose if you are incredibly ---- you would want to do it but know that I ended up with no CEL and the only difference from a factory manual car is it will only start in neutral; clutch depression doesn't make a difference since the auto car only uses the neutral safety switch for starter engagement lockout instead of the clutch switches. You could probably wire in the clutch safety switch instead of the neutral switch but that entails adding wire and making it look neat and clean. Ain't nobody got time for that. Another thing I saw a lot of was people saying you will need the ignition lock cylinder from a manual car because of the park lockout feature on the auto cyl. I wouldn't want separate keys for my doors/trunk and ignition and didn't feel like changing them out from my donor car. So disabling the lockout was the best option and it took about 5 minutes. Remove the cable from the mechanism and take the bracket off the cable. Pull it very hard from the shifter side. Now the cable is out. Next take a cotter pin and put it through the hole in the shaft the cable attached to. Then run a zip tie through the head of the cotter pin and around the mount for the lock cyl. and tighten. Now the feature is disabled.
What you actually
need from a 5spd donor car:
Clutch pedal assembly
Brake pedal (or cut yours)
Clutch master, slave, line
I have a pretty average garage with average tools. Jack and jack stands. 1/4 3/8 and 1/2in rachets. electric impact. you know, nothing special. The job took roughly 10-12 hours total and that was with many beer breaks.
I hope this saves someone from spending a lot of time doing stuff they don't need to and more importantly, money.