That should have been one of the first things you investigated.
What's with the pic of the engine sans oil pump?
Gen 3 up is nothing like swapping a manual in a Gen 2 down.
Short answer - the car's systems are on a CAN-bus and there are things like immobilizer, neutral switch, park lock, reverse lights, ABS/VDC communication, ............ All these are wired together through the main harness.
You need the compete wiring harnesses, computers, and instrument cluster for a manual car. Preferably from the same car. Then the keys have to be programmed to the computer for it to start. Getting the computers and harnesses will also solve the issue with any emissions issue fault codes that would come up due to trying to rewire existing systems.
Put the auto back in, sell it and find a manual car.