I have just reread the last 4 pages of this thread.
1. It appears that the temperature sensor and the sensor wiring is good.
2. The pump is working
3. the pressure in the rail is correct
4. you have have plenty of pump flow
5. You have spark
6. The engine will start and run a second or two with the pump unplugged after it floods
7. The MAF appears to be working correctly.
Despite all the above, the engine is flooding. Unless the ECU is whack, the only other cause would be injectors that are open all the time.
The injectors are opened electrically by a GROUND pulse from the ECU. They are all connected in parallel in the harness. One terminal on each injector is connected to 12v whenever the bike is turned on. The other terminal is connected to a circuit in the ECU that controls how long the injectors are opened. The circuit has some transistors that act as switches connecting the injectors to the ground.
To test this, you need to get a 12v LED and some alligator clip test leads. Disconnect the injectors from the harness. Connect the POS wire of the LED to one of the injector connector terminals and turn on the ignition and touch the NEG wire to ground. THe LED should light. If it doesn't, reverse the connections and try again.
Once you can make the LED light, connect the NEG wire to the other terminal on the injector connector. Turn on the ignition. The LED should be out. Hit the starter, and while the engine is cranking the LED should blink.
I suspect from what you have been seeing that the LED will stay lit, meaning that the injectors are being held open, dumping uncontrolled fuel into the cylinders.
If that is the case, the problem could be the ECU, or a problem in the injector harness.
The next test is to unplug the big connector on the Jetronic unit. Take the POS wire from the LED and connect it to the Battery + terminal. If the LED lights up, you have a short to ground in the injector harness.
If it doesn't light up, reconnect the plug on the Jetronic. If it lights up, there may be a problem in the Jetronic. Turn on the ignition. Does the LED go out? If it stays on, the Jetronic is probably whack.
I have read about the output transistors in the Jetronic going bad. It doesn't appear to be a common problem, but it has happened. Someplace I read where there it can be repaired. Something to do with resoldering a broken connection or something like that. Maybe Laitch can find the link. He's amazing at stuff like that.