Update -
While testing the IR transmitter wiring (checking for loose/broken connections) I did find a place in the wires where it was pinched. My guess is when I was reassembling the engine shell to the chassis I pinched the wire and shorted the IR transmitter to shell ground. The wire did not show any obvious physical bear wire. While the wires and connections all tested good, my thought was either the IR transmitter diode or the main control board RCMC was bad.
I completed an engine reset following the manual (changing or reentering the engine ID resets this engine to factory default). No change in operation.
I received a new IR transmitter from Lionel parts and sure enough, the IR transmitter was bad. Engine is now fully operational again. 
