The other day I went to start up my 2005 FatBoy (fuel-injected with a Power Commander V, Ness big sucker and V&H Big Radius pipes) and it seemed like the battery was low and it barely turned over, but it did start. However, it seemed as if one of the cylinders wasn't full on and the engine light came on. It almost stalled out at idle and the power of the engine was way down under throttle. Then I went to start it again about half an hour later and everything seemed OK.

Any ideas as to what this could be? Think it will come back to haunt me?

 

i would deff. ck the battery, this could cause low spark and spark plug fouling.

 

You can take your battery to Autozone and have them put it on a load tester. If it has low voltage under a load then you have a dead cell and battery needs replaced. I would rule this out,first.