Bike is an ‘03 FLHR 88in with under 15k miles. Detailed mods are below, work done by myself last year, if not mentioned below then it is stock, I have put on at least 4k miles since doing this work.

When I purchased the bike two years ago the engine always seemed to have a misfire. Confirmed misfire is from the rear cylinder. Rear cylinder runs like poot, poot, poot, POP, poot, poot, POP, poot, poot, poot, POP, poot, poot, POP. It is noticeable when pulling away from stop, cruising at ¼ throttle and on decel. It really makes for a rougher ride than I would like. When starting bike from cold it often gets into a rhythm that sounds like a thumper, running on one cylinder.

I just installed fresh Autolite 4164 with .040 gap and swapped plug wires front/rear, still having the same problem. I also confirmed resistance on the coil and wires are within spec. My next step is to test different plug gaps. Maybe go up to .045 first. Any other thoughts here? I feel like it is getting worse.

Fueling cam plate & oil pump
Replaced inner cam bearings
New style Roller cam chain
Andrews 27 cams
S&S lifters & adjustable rods
Cobra true duels
V&H Big ovals
Screaming Eagle air kit
CV Performance emulsion tube & sporty needle
195 main, 48 pilot, 2.5 turns out on mix screw
Replaced intake seals, no leaks

 

Seem to be running into the same issue on my 2002 Heritage Classic. I've done a small handful of engine mods such as S&S 510g full cam chest kit, full dual system exhaust, S&S Stealth air cleaner, screaming eagle performance plugs/wires, and and dynojet tuner. Did you ever figure out what your issue was? I think mine is a bad air seal around the rear fuel injector o ring. I already changed out the intake seals and now ether will almost stall the bike if i spray around the injector. I've heard MAP sensors are bad for this as well, but i tried my hardest to make sure the ether was on the injector. Any thoughts or ideas?

 

Update
The tune in the PCM was corrupt , to it to a local shop who reflashed the PCM , that fixed it , thanks for all the Suggestions