Car starts only when AFM is unplugged? Options

[6G94celica]

So I had my car at a shop a couple months back and they shorted out my battery on my transmission. I have my battery relocated and hadnt gotten around to putting a fuse inline. Anyways what initially happened was the car drove but wouldnt produce any power under boost. I took it around the block and parked it to try and figure out the problem. Since then the car wouldnt start at all. The car had no check engine light when i was at ON. I checked by grounding W terminal on ECU and the light and wiring are fine it turns on. I then checked power to ECU and ECU grounds, all good. I was searching through the wires around the transmission where the short occured to see if any had been burnt through and had my intake and AFM removed from the car.

I noticed that when i turned the key to ON with the AFM unplugged the check engine light came on. Turns out the damn car started fine with the AFM unplugged. I didnt let it run more than a second because i didnt think that it was even supposed to run without the AFM plugged in. Does anyone know what caused this or what i should do. I thought about picking up another AFM but want to explore other options first.

Also i should mention that the power shorted on the topside of the transmission and the AFM sits on top of the transmission. Im thinking that the AFM was fried and the ECU reads it as a bad sensor and wont let the car start.

Any help is greatly appreciated