I have Woods 555 cam, Fuel moto EFI tuner, SE air cleaner, Vance & vines true duals in my 96" motor. It has been running great for the past 18 months since making the modfications. Dyno was at 86hp 103tq.
The problem: When engine has cooled for the first 10 miles or so I never see the problem it runs great. After if warms up when I turn the throttle I don't know what kind of performance I'll get. The power may be good to poor or somewhere in between. The same when at cruising speeds if I hit a grade it may pull good or I may have to drop to 5th for maintain speed. I took it to a HD dealer when I first noticed the problem for a tech to ride it. It set about 45 minutes and cooled before riding and when he returned said the bike ran strong low end, mid range and top. They checked the fuel pump pressure and it checked 60+ psi which was good. They suggested it may be the power commander and to unhook it the next time it acted up. I contacted fule moto and discussed it with them and based on a few suggestions don't see and problems. I have since unhooked it and the problem remains so have ruled that out. When I experience power loss the motor never pings, spits, sputters or coughs. The motor just won't pull.
It has been suggested it may be the battery and the ECM needs 11.46 volts to operate properly. I have the original battery (68 months old) I don't mind changing it but checked the off voltage at 12.5. Started it and checked at 14.1 volts, left the stereo on for 30 minutes with engine off and dropped to 12.25 volts then cranked with no problem. No engine codes are given. Any advise would be appreciated.

 

Could it be something as simple as an issue with the Throttle itself?

 

Cables are new and I have checked and verify that the throttle position sensor is working fine.

 

Might want to throw this question out to the Touring Forum here: https://www.hdforums.com/forum/touring-models-11/

 

Have you checked the speed sensor? I had a problem just like this and the dealer replaced the sensor and its been fine ever since.

 

Temp sensor, Throttle position sensor...........Even if it tested good, Look for & clean all suspected grounds. Any parts of the wiring harness that clip together, pull them apart, clean them & firmly push back together.
It would be nice if you could swap coils with a buddy for a week & try that as well.
Hatch.

 

when ya key on, do ya wait for the check engine light to go off b4 ya start?
one MUST wait for the check engine light to go off b4 starting. this is stated obscurely in the owners manual BUT was strongly reiterated by my dyno guy.

 

I had something similar on my 07 Eglide. Turned out the elelctrical cable to one of the injectors (front I think) was pulled too tight and the wires started to break at the connector. It would make the injector intermittently cut out.