Nick,

First, with battery disconnected, reach up on top of the target plate and remove all the dust. This builds up over the years and never gets cleaned. Also, make sure the prox switch is clearance is about 6 mm above the target plate. Check the new encoder harness. Make sure the ground strap is bolted in place. If you have a wire hanging, this is your ground strap. If it is not connected, will cause codes. Should you continue to have problems, may have bad encoder. Good Luck.