I recently bought a 03 Electra glide classic, bike is missing some! The bike sat up a while so I thought there may be water in tank, so I've tried running some water displacement thru it! No luck! Cleaned air filter and installed new plugs, no luck! It acts like water in fuel missing every so often, running great at times and bad at times! No pattern! Need some help!

 

Try running some seafoam in the gas tank, that usually works good. you can pick that up in any automotive store. Will it idle ok or does it keep dieing out?

 

The "running good at times" leads me to think that its not a fuel issue.

Before you spend any more money, check your battery and ground wire connections, and make sure the battery is hold a good charge.

I had a 2000 Ultra that developed a steady miss at a constant speed/RPM that nearly drove me nuts!

I tried most everything from spark plugs/wires, a new TPS, intake seals and then I started suspecting that it may be either a bad fuel injector wire, or worse, the ECM.
The indy working on my bike couldn't get the bike to "code" until he put a new Engine Temperature Switch and the it "coded".
Turned out to be one of the things that I had originally suspected, the ECM!

I hope yours isn't bad (they're expensive) but that sure corrected my problem.