I have not had a TBI setup for about 6 years and I'm a little rusty. Trying to help troubleshoot. Looking at the list views in tunerpro (using the $42 I downloaded from here) towards the bottom is "Crank Sensor Pulse". Should that be toggling Yes/No while the engine is running?

Symptoms seem to indicate an ignition problem and I am wondering if the ECM is losing that signal from the ignition module.