I have a harley davidson 2003 electrglide and it is missing ,what would be the cause?

Spark plugs are a big deal on motorcycles. Use the same ones that originally were installed in the bike (gap to spec.). If the problem persists, focus on the Ignition Control Module and coil.

Thank you ! What about fuel pump would that make it miss and cut out as well ?

That's a possibility but less likely--most of these problems are electrical related. Check any screen and replace the fuel filter, if it hasn't been replaced recently. Also, ensure the battery is fully charged (charge at 2 amps or less) and the battery terminals and cable connections are clean and tight--coat with dielectric grease.

A sticking or faulty fuel injector or faulty Engine Control Module (ECM) could cause a misfire as well.
This needs hands-on diagnosis while the misfire is present.