Its because the signal to power down the car comes from the ignition and is basically confirmed by the ECU, you have that unplugged. There are relays behind the fuse panel on the drivers floor board that kill the power to the accessories in conjunction to the relay panel on the drivers side in the engine bay just behind the headlight. What motor are you planning to install in the car? Because with the engine harness out of the car things like your gauge cluster won't work, so you'll have to find a solution to that issue depending on the motor.
Here are some diagrams I've found useful over the years.
These are courtesy of Hashiriya415 most recently, but they are from a FSM
And this one helps a bit too. Its my personal favorite.
