Viper 5901 Remote Start/Security System, Crank No Start, 2006 Scion tC

Ok this is gonna be a long one and I apologize for it. I have a 2006 Scion TC, manual 5spd. I bought the car 10yrs ago with the viper 5901 system installed. It worked fine with now problems. I need up blowing the engine and it sat for a couple years. When it was sitting, someone broke into it when it was armed. They got the door open and unplugged the antenna/valet button and then the battery to silence the alarm. After sitting for about a year, I finally replaced the engine with a running/compatible engine, and yes I'm a mechanic and have swapped engines before. Now that the engine is in, I try to start it and all I get is crank no start. I also tried the remote start thinking it may work but all I get is 8 flashes of the headlights. I've looked everywhere and when it got broke into they never cut any wires. Also one other thing. My LCD 2 way transponders battery fried while the car sat, which was the remote to arm the system. so all I have is the 1 way remote. Idk if that would have an effect. Does anyone know if the alarm going off and unplugging the valet button would set off the immobilizer or any other security feature, could the brain be bad from sitting so long? It has the TBXkey bypass for the immobilizer. And like I said it worked fine before it was broken into. Any help would be very much appreciatedTrevor Webster

did you swap ecu's? since your a mechanic, I assume you checked the basics, you have fuel and spark?

No need to swap ecu because it's the exact same engine. Have spark but no fuel. Cleaned injectors and fuel pump is working. Unhooked fuel line and drained all old gas and put fresh in alsoTrevor Webster