Hi, I run a 99 Road King Twin Cam. The only thing in the motor Harley are the cases, oil pump, and cam plate. The FI is S&S Tuned Runner and the computer is S&S VFI.

It's an S&S 116" setup with Woods TW6HG cams.

Problem: 80 miles from home yesterday and after the bike was sitting for about two hours, I went to start the bike and it was running on one cylinder. Read cylinder was firing, not running. Changed plugs, no help. Had bike towed home.
Today, I started the bike and it ran fine, for a few minutes. When it started to warm up it would not idle. Themore I tried to keep it running, the worse the idle got (not missing, just low idle).

My "gut" tells me it's a sensor problem.Thought I would ask around before I started trying to troubleshoot with the manual as a guide. Anyone had thisproblem? Anyone have short steps for troubleshooting the sensors?

Thanks

 

If the rear cyl was firing and it has compression it leaves fuel. Check compression, check wires for breaks to injectors (will feel soft right at the connector)

 

you said after it warms up it runs worse.I would check the engine temp sensor. I don't know S&S VFI, but on the Daytona Twin Tech EFI, this throws a "code".Did you check with S&S??