02 f4i Won't Start
 

Hey guys, I could really use some help diagnosing why my 02 f4i won't start. I bought it last September, rode it a couple times and then had to put it away for the winter since I live in MA. A couple months ago when I first got my bike out of the garage to start the season, everything was going great. It would start right up and it seemed to be running relatively well. I rode it twice in a few days and then decided to do an oil/filter change (Rotella 5W/40 and K&N filter) and replace the air filter (washable K&N filter).
When I went to start it up for my next ride it was really struggling to start. It only started once I gave it some gas and if I let off the throttle the revs would drop and it would stall. After doing this a couple times, the engine wouldn't even fire, but it was still turning over.
I checked the FI codes and it was throwing 1, 2, 7, 8, and 9. I think that most of these were from the previous owner and had just never been cleared, but I checked out all the codes anyway. 7, 8, and 9 correspond to the ECT sensor, TP sensor, and IAT sensor respectively so I checked to make sure that the sensors were all plugged in correctly and were returning the appropriate resistances. Everything checked out. None of those sensors should have prevented the bike from starting though as the ECU would just simulate a preset value; correct me if I'm wrong.
So next I checked the MAP sensor for FI codes 1 and 2. It was plugged in correctly and the vacuum hose was connected; it was also returning the correct resistance according to the Haynes manual. I did notice a small tear in the vacuum hose near the connection to the MAP sensor so I used some Krazy glue to seal the hole and then tested to make sure that air could still flow through the tube. The bike still wouldn't start. Fuel pump primes, the engine turns over, but it won't fire.
Checked the kickstand sensor, clutch sensor, and engine kill switch and they were all functioning correctly.
Next, I checked the spark plugs and they were a bit fouled so I replaced them with some NGK Iridium plugs. Tested for a spark on cylinders 2 and 3 and I wasn't getting one. At this point I didn't know what else to check so I decided to buy a used ECU off ebay. When I got it, I swapped it out for mine and it started right up! FINALLY!
I thought at this point that I had finally solved my problem and I was ecstatic. Took the bike out for a few rides including one almost 70 miles and when I filled up the tank I calculated that I had only gotten 18mpg. Did some reading online and it looks like generally this points to a faulty fuel pressure regulator, so I ordered a new OEM one and swapped it out. Bike started up no problem afterwards and the exhaust was smelling a lot cleaner, no unburnt fuel smell. I didn't have time to go for a ride after I swapped out the FPR so I only had the bike running for maybe a minute.
The next day I went to take it out for a ride and the bike was struggling to start up again. Same symptoms as before. Gave it throttle and it would start, but only if I kept on the throttle. As soon as I let off it would die. At this point I checked the headers and noticed that only cylinders 1 and 4 were firing; 2 and 3 were significantly colder (could touch without getting burned). I decided to put the old FPR back on, just in case the new one was faulty and it still wouldn't fire. Now the bike won't start up at all. Fuel pump primes, engine turns over, but it won't fire.
Sorry for the novel, but I have no idea what to do next besides rip out the main wiring harness and check every connection. Any thoughts or suggestions would be hugely appreciated!

TLDR: Bike won't start. Replaced ECU, bike starts! Replaced FPR to improve gas mileage, bike no longer starts. Help.

Does the bike have a power commander on it?

No power commander

Did the ecu numbers match to the original one?

Maybe you got one that uses an oxygen sensor?

Yes, the ECU numbers match; it is a 38770-mbw-a12, not the California model with the O2 sensor.
The fact that replacing the ECU fixed my problem initially is really messing with me. It leads me to believe that I have some faulty wiring somewhere along the line that is either burning up the ECUs (is this possible?) or it was just that I inadvertently shifted some wiring around while replacing the ECU that fixed the issue and the ECU itself was never bad to begin with.

Is your F4i coil-on-plug? Or is it 2 coils running on wasted spark?

Did you ever pull the NGKs and look at them since you put them in? If so, what did 2&3 look like?

It has to be something that changed when you changed the air filter. It ran fine before, but not after......

You did take the cap off the fpr before installing it, didn't you?

Looks like its coil on plug. Are you sure the correct correct wires from the harness are going to the correct coil? Whenever I hear that 2&3 aren't running, that's what I jump to.

Its simple to mix them up after changing plugs, it'll be intermittently hard to start and it'll kill your mileage.

I've got separate ignition coils for each cylinder, so that means coil-on-plug right?
I have not pulled the new spark plugs since I installed them. I'll try to do that tonight and take pictures.
Do you think the ignition coils on cylinders 2 and 3 could be bad?

No. Two at the same time would not be very likely.

To verify, you could swap them with the other coils and see if they fire or not.