I am still no closer to having this problem figured out. I got my parts in yesterday (new fuel pump and fuel filter) and took it for a ride this morning and it is running the same way. The hoses on the inside of the tank looked like new. The only thing I can think is that I put on screaming eagle slip ons a few weeks ago. I left the stock air filter on. Is it possible that it is running lean? Maybe need to map the injectors?

 

If that ends up being the case then just talk to Jamie at fuel moto and get a PCIII, you have the older MM EFI and they can be a Pain and almost nobody knows how to tune one. The PCIII fixes that part. Mine finally started doing some of the same things yours is doing and i took it off and put a carb on mine runs great now.

 

Run some seafoam through it.

 

Hd had a problem with the convoluted fuel lines inside the tank but id have to believe it should not be an intermittent problem. I guess if all else fails though you can check it out .

 

What controls the choke on a fuel injected bike. The more I thought about how it runs, it runs like a carberated bike that the choke was left on. Is it possible that the choke keeps kicking on and off (if they have a choke).

 

Try to clean the throttle body with TB cleaner.
Maybe the engine temp sensor is going also.
Any codes?

 

Could be the head temp sensor it will make the bike run very bad. Is it blowing black smoke when it is acting up? My bike had the head temp sensor go bad it acted like it had a choke turned on. When it's first started it would run fine once warmed up a little then it would miss, have no power,and smoke.

 

That sensor may very well be the answer I am looking for. Mine runs almost identical to how you described. Runs good when cold then when it starts running bad it has a little bit of black smoke. Where is this sensor located? I have not yet taken the bike to a shop so no codes.

 

the head temp sensor is in the top middle of the front head.I had to take the fuel tank mounting bolts out and raise the tank to get clearance and it will be easier to remove the 2 coil bolts and move the ignition coil a little to get to the sensor. If you think it is the sensor You can do the sensor your self its not hard to do and a lot cheaper than taking it to the shop as they charge out the rear for labor more than the price of the sensor which depending on where you get the sensor can run anywhere from $50.00 to $125.00. If you have more than one shop locally check on the prices to get the best price for the sensor. Good luck! I'm thinking replacing that sensor will fix it.
Norman

 

It may be a little early to say but I believe the sensor fixed it. Just replaced the old one went out for about 30 minutes and had no problems. Thanks everybody for the help.