My Step Dad has an 05 EFI Deuce with 5000 miles.
Only mod is cycleshack slip ons that he's had on for about 1500 miles.

it ran perfectly until last weekend when it started missing, stuttering, acting as if it was going to stall when stopping, etc.

The air filter was a bit dirty, but not bad. the only other thing i noticed was that the front cylinder pipe has a brownish tinge in the tip and the rear cylinder pipe is a normal dark grey / black.

any ideas?

 

did you pull the spark plugs? if so what did they look like?
did your Step Pops have anykind of fuel management improvement (ie...download/sert/pcIII) done when he had the pipes installed?
HD's run on the lean side from the factory or so I'm told. so its very possible that the pipes caused a lean run condition if the fuel mixture wasnt adjusted.
1500 miles of running lean is more than enough to hurt it unfortunately

 

Was it cold out? I run an open K&N filter and when its cold out it ices up, and starts running bad and wants to die. Let it set for alittle while and it would start right up and run fine. Never mind I just noticed you said EFI.

 

did not pull the plugs yet.....he is taking it in for oil chg and will have the guy look at it then.

is the difference in the pipe color due to a lean cylinder?