RX7Club.com - Mazda RX7 Forum - Bypassing Automatic Safety Features

I don't think you need to bypass it you just need to get the connection right to the ECU and then it will work like a manual car. The wiring should be there but may need to be extended/ran to where it needs to go. I posted this in your other thread:
Did the car start fine when it was an automatic? If it did, I don't see haw swapping to a manual would cause you to have to change the wiring to the starter as even though the starters are different the wiring to the starter should be the same. Same goes for the ignition switch. What is different is how the ECU gets the signals that tell it that either it is in neutral or park for the automatic or the clutch is pushed in for the manual. Without these signals to the ECU it won't start. The differences I can find in the FSM are found on pages F1-79 and F1-80 in the ECU connections. From this it looks like you have to find the EC-AT control unit inhibitor signal(this may come from the EC-AT control unit though pages K2&K# show and inhibitor switch on the auto trans so that may be your wire ) and connect it to the to the Neutral Switch on the manual trans. Then find the one that connected to the Oil pressure switch on the AT trans and connect it to the backup light and 5thgear switch on the manual transmission. There is a M/T switch that looks like it had no connection in the auto. Hopefully you got it with your pedal assembly as it tells the ECU the clutch is pushed in so it will allow the car to start. I can't find where this was connected or if there was a connection on the auto. This may not all be right as I haven't done it on an Rx-7 I just looked at the FSM. I did do this swap on a Toyota pick up and I did have to find the connections on it as and rewire them as I describe here to get the truck to start. No change to the starter or ignition on it either.