Matt:
Mellow out. Put all your new bits back on, then do a full ECM reset (disconnect battery for at least a minute). Something put the tranny side of the ECM into "limp home" mode, probably the TPS in the throttle body. Do you currently have a CEL on? If so what codes is it throwing?
By the way, it would help to know what it is we are trying to diagnose. Year, Buick, Chev, LO5, LT1 etc.
Bill