i have a 2001 softail standard efi with 13k miles on it it has been progressivley running worse and worse. im an auto mechanic and have been for 17 years therefor no one else has ever touched my vehicles when it came time to fix or hot rod one of them but this thing is really bugging me.for starters i have vance&hinse big radius pipes an arlen ness big sucker air cleaner kit and a revtech dfo unit all of which have been on the bike for almost 3 years.the end of last summer i noticed it was starting to lose a little umph, like tune up time so i changed plugs,wires air filter,oil&filter,but it made no differance this spring it also developed a vibration in the drivetrain at 2200 rpm, i also noticed that the pipes dont sound as crisp or deep as they once had since this issue started.long story short iv replaced clutch hub and basket with bearings,main shaft bearing,engine temp sensor,new spark plug wires,intake gaskets,primarychain adjuster with a hayden m6auto adjuster,tightened all motor mounts,tested compression,checked fuel pressure,checked injectors and ignition coil resistance, i also plug it into a pc running twintec software to check my ecm parameters and codes but everything was fine. best way to descibe it is it runs and sounds like it has low compression on both cylinders but its got 140 psi in both if anybody has any ideas please let me know i dont want to take it to a dealer.

 

Almost sounds like valves but you said it has good compression.
One thing to look at. Nothing has crawled into you pipes and created a nest has it? Sounds funny I know but check it out.

 

Fouled fuel injectors? Maybe you need a new fuel filter? I was going to recommend that you remove the TFI/DFO and try running without. Isolate one thing at a time and hope that your not seeing a syptom of more than one cause. If the DFO don't do it, yank the mufflers. I've had mufflers rust and break apart internally causing exessive back pressure. Make sure that there are no air leaks or obstructions in your air intake and throttle body. If none of this works, you probably have a bum ECU.
Good luck!

 

Check this OUT and yes I swear by SeaFoam

https://www.hdforums.com/m_488477/tm.htm

Hope thats all you need

 

My cousin had a similar problem on his bike.It turned out to be a vacuum line running from the tank to the carb?I think thats what he said.He said at a certain RPM it sounded and ran like it was running on one cylinder.

 

ive found the problem my arlen ness big sucker air cleaner was cast wrong, the breather bolts didnt line up exactly causing the throttle body to be pushed towards the rear cylinder causing the front intake gasket to open up and leak .installed second set of intake gaskets, centered the throttle body using factory air cleaner base and the thing runs great thanks to everyone for any help givin. keep the shiny side up!!