I have an 89 f250 2wd 7.3 idi with e40d auto tranny. Bought a king ranch and dont drive this one much anymore but a rat got under the hood(he's dead now) chewed up a bunch of wires at the glow plug harness and temp sending unit. Now the tranny goes into gear pretty hard shifts extremely hard and the OD off light blinks consistently where should i start looking here? Truck has 110k miles and everything ran just fine when i parked it about 3 months ago

 

Blinking OD-OFF light means a code is stored. Start there.

 

Now earlier i went out and looked again and i noticed a black box like plugin on the drivers side of the injection pump is this the throttle position sensor? The wires running to it from the harness are chewed off if so im assuming thats the reason behind the shift issues

 

Yes, that is the throttle position sensor. You need that to make it shift correctly.