Seems like you're so close!
Do you know what input the MAF is sending to the PCM? How about the MAP? I think an Engine has one or the other ... so maybe no MAP on your Engine (since you said you cleaned the MAF)? If the MAF input is bad ... maybe that could be causing the ECM to flood the Engine (??) ... although you'd think it'd be smarter than that, right? Also, along these lines ... do you know if the Throttle Body Butterfly is even opening? Maybe it's closed and there's no air getting in? These values are in the OBD-2 data list, and it's possible a Reader's "logging" functionality might be able to capture them during a "Cold" Start.
What about the O2 Sensors? They're typically only used once the Engine goes to "Closed Loop" ... which occurs after it heats up ... so not during "Cold" Start (which is where you're stuck) ... but they also have "heaters" on them ... which means they might be getting referenced during a "Cold" Start?
Of course ... the other "elephant in the room" is the Timing of all these Signals. What you really need is a Display showing all the pertinent signals superimposed on a single Trend ... so you can verify the Timing of all of this (i.e. ... you have Injectors firing, but not when the Fuel is being Injected ... or when the Plugs are Firing ... if that's even possible). What if the Cam Sensors (or Crank Sensor) are "working" but not reporting accurately because what they're "watching for" isn't accurately mounted itself (is this the "Reluctors" at the end of the CamShafts ... can those get "spun" ... or what is the Crank Sensor watching ... some piece on the back of the Crank Balancer ... but you didn't touch that, right)?
I'm sure the Dealer could just crank your Engine for a few seconds ... while running his Data Logger ... then have all these input data points (Crank Sensor, Cam Sensors, Plug and Injector Firing signals, MAF sensor, Throttle Position, O2 Sensors ... appear on a Graph with their square waves... then look at how they "marry up" ... and say ... "Oh yeah ... here's the problem right here ... ".
Should really only take them a few minutes ...