Sorry I've taken so long to finish up this thread.
I did some preliminary troubleshooting but didn't make any progress and ran out of patience. I had the dealer pick up the bike and trailer it to their location. Tech said the bike was only running on one cylinder and when he disconnected the TFI wires to the fuel injectors and hooked up the original factory wiring, the bike ran great.
I had them remove all of the TFI hardware and install the HD Stage One download to the ECM. I have ridden for about three hours since then with absolutely no more issues.
I'm not sure where the problem was in the TFI system so I will return everything to Dobeck if they want it for diagnostic purposes. Otherwise, the weather's getting cool enough that I plan on just riding it with the Stage One download for now.