Immobilizer problem

So I bought this car and I replaced the entire inside of the vehicles interior. This includes the dash, carpet and roof (sunroof as well). The car started before I did the switch and when I switched the dash the car stopped wanting to run. I accidentally replaced the PCM at the bottom of the dash. I put the original back into the car and the car would not even start, turn over, or anything. Every part to the dash has power. Every component to the engine is getting power. I had a mechanic check all the fuses and relays and they are all good. So I called a lock smith in to code a new key into the car and possibly flash the PCM back to the vehicle in order for it to run properly again. The guy got to my shop and said that the immobilizer needed to be hooked up for him to code it properly but I cannot plug it in because the wire for the immobilizer does not fit for whatever reason. (May have been replaced and coded/bypassed before). And yes, the car was running before with the immobilizer not functioning obviously because its wire could not have been plugged in. The doors are also off the car and the trunk does not have its latch connected to it. (It is going to be a custom car). I am totally mixed up on what move I should make next and I am in dire need of help to get this car running and drivable again.
If you have any further questions on what I did to the car do not be afraid to ask I know every bit of everything I did to it.
Help!