I recently acquired a 1995 30th Anniversary Edition Ultraclassic with only 5000 miles on it.. the bike is in excellent condition, but set in the previous owners garage for the past 3 years. The problem with the fuel injection is this:

The bike, as far as I can tell is all stock. The engine starts right up, and idles well. After letting it warm up for a few minutes, and accelerating in first gear, between 2500-3000 RPM the engine stutters, skips, and sometimes stalls. It acts like it's not getting any fuel in that 500 RPM ... if it stalls, it does start right back up...if I can coax it past 3000 RPM it runs fine...inless the RPM drops below 2500 then the symptoms reappear. They are less severe as the engine gets more heat into it...but don't fully go away.

I've been told the cause could be bad intake gaskets, clogged injectors, bad or unadjusted throttle position sensor.. bad ignition, and so on.

I would like the thoughts of those who have experience with this system. This is my first experience with the magnetti-marelli EFI system.

 

If you spray carb cleaner around the intake when it's idling, and the idle doesn't change, it's probably not a vacuum leak.
It could be a few different things. Maybe take it to a dealer Or MM specialist. I had problems with mine, and after tinkering with it, I could never get it right.

 

Was the bike stored with gas in it?
You should probably run the M&M EFI 101 on it. That is:

Check for any stored codes.
Inspect battery cables, make sure they are clean, not corroded, and tight.
Inspect the insides of the tank for loose liner, or dirty filter (I doubt if the filter is dirty with only 5,000, but may need replacing if the bike was stored with fuel in it)
Resynch the IAC to the ECM. There is a key ON/ OFF sequence that you can do after disconnecting the battery for 30 min.
Look for any tan goo dripping down from the bottom of the nosecone. The cam position sensor will melt when it is bad. Another thing not likely, but you never know with a bike that has been sitting.

The 1995-96 ECM is a bit different than the 1997-2001. You will need to swap it out before you can add a tuner, but I would get the bike right first.

 

Call in the Evo section, where you should get some helpful tips.

 

UPDATE: problem turned out to be crank position sensor cable connector under right side cover was disconnected. Reconnected and bike now runs great.