for a temp fix you could take the valvebody out and plug th harness back in and tuck it up in the engine compartment in a big zip lock bag.
Its been a while since i did a 5r110 to a stick but i do remember its a certain voltage that you have to send back to the pcm to tell it that the trans in neutral or park, You can get a prtentiometer and put it inline and turn it until it starts of get the correct resistor and install it inline between the refrence voltage and the signal pin in the trans wiring harness.