I think Ryan may be onto something here... What did you do with the two wiring bundles and connectors at the top of the tranny? The JC Sports kit instructions included steps to unscrew the brackets and loop the wire bundle on top of an aluminum A/C line. Since these wires carry virtually all the signals that you're getting codes for, I'd suspect that something happened to these wires and/or the connectors.
Weren't you supposed to make a trip up here so I can take a look at it? Or were a CF hood and wheels more important?