Edit , my bad. I guess you can get a 87 performance tune. I thought the 87 was called the economy tune in a canned set.
Trans tables rely on MAF and TPS info. Usually a TPS problem generates DTC, but not always; same goes for the MAF. The bad about that is they have to be about spent in order for that to happen. With an 06 3 valve, in this case, I would pull the rail/leave the injectors connected to rail/lay a bunch of rags down(just in case)/ reconnect the battery/ Turn key to run = charge the rail.
If you have a bad injector, which is common in the 05/06 model years, it will be leaking with rail charged.
You can also test for PCM driver signal to injector, but that's not a common problem. Stethoscope each injector while running, if it's clicking, the driver's fine.
Make sure the battery is FULLY charged - over 12 volts, not under.
It does this in the same EXACT way, every time? Idunno, it could be over-fueling. The very first thing to do is look thru all the 2006 3 valve TSB's, there's a ton of them lol. Those can be real helpful. You might want to get your stock tune re-flashed, -I know there's updates @ Ford. I think it will cost yuh 80 - $90 tho. Not sure what effect that may have on your other tunes if any. Yea, TSB's first.
BTW- Make sure you fully reboot, -I pull the PCM fuse/fuses along with a battery disconnect for KAM erase/reset.
Good Luck
