I have been having problems with the bike starting at times for quite a while and a lot of tanks of gas. Also the gas mileage has dropped pretty significantly in the city. I used to get 32-35mpg in the city and now I'm lucky if I get 25mpg. I can't even get to 100 miles before the light comes on and it always comes on right around 1 gallon left.
Sometimes I go out to start it and it cranks and cranks but won't ever fire up. It would then drain the battery down so i would put it on the charger and let it fully charge then it would usually start up after that. It wouldn't last but a week or week and a half though then it would be back to cranking but not firing up. Sometimes though it would come straight off the charger (fully charged) and still not fire up although it would crank until I ran the battery down.
I took the bike off the charger last Saturday and it started fine. I rode it 3 times to work during the week and was keeping tabs on the voltage in the morning. It seemed every day it dropped about .02v from the day before. This morning it read 12.75v but it would only crank and not fire up. I put it on the charger for about 45 minutes then came back and it started right up.

Thing I've tried
I bought a new battery from Advance last February so it's almost a year old. I suspected maybe it might be going bad so I had a couple of Advance stores test it and I even had the Harley dealer test it on their new machine (took about 30 minutes) they all said the battery was fine.
I have cleaned the battery cables, made sure they were tight on both ends.
I put a multimeter on the battery while the bike was running and it seems to be charging fine, getting over 14v while running.
Cleaned the IAC on the throttle body.
Spark plugs were replaced less than 1,000 miles ago (this was happening even before I replaced them)
Checked spark plugs and they aren't fouled at all, in fact they are extremely clean.
Pulled plug wires off on both ends and made sure they were securely connected.
Tried putting seafoam in the gas tank

I know I should have checked for spark at the spark plugs when this happened but for some dumb reason I never did. I kept thinking it was a battery or cable problem.
This has been going on for a while and has made me stop riding as much so I finally had enough today and took it to the dealer to have them look at it. One guy told me it sounds like the crank position sensor. What is weird though is that after it does start it seems to run fine, well except for the decrease in gas mileage.
They are going to let it sit a couple days in the shop before they look at it since it seems to happen after it sits a few days. Hopefully they will be able to reproduce the problem because it doesn't always happen although I don't think I've gone 2 weeks without it happening and having to put it on the charger from running the battery down trying to start it.

I plan on coming back to update this thread but in the meantime, does anyone have an idea what might be wrong and is the reduced gas mileage a coincidence or do you think it is also a symptom of whatever is wrong?

 

I am a new HD owner and know little about these motorcycles but I am learning all I can. I do believe taking it to your dealer is the correct course of action. It may cost more but I`m sure they will be able to diagnose and fix what is wrong. I, too, will keep reading to be updated. Good luck.

 

It does sound like the CPS. They are easy to replace and relatively cheap if I remember right. I hate intermittent problems. They are what separates the good mechanics from us hacks...

 

Long time ago, I had a battery check out as "good" in 2 different places. It would fire the bike up but compression would stop it cold, then it would turn past it and stop again. It always started tho! Got pissed and bought a spanking new Gorilla of a battery and it spun the starter like crazy! End of problem! A weak battery sometimes will have enough grunt to spin the engine but not enough to run the ignition system too! If it is charging okay (14 volts sounds good), then your well tested battery may be weak after all. You might check your frame grounds and engine ground...some times they'll screw you. My .02 cents. Good luck!

 

Maybe a fuel leak inside your tank, seems to be pretty common. The fuel hoses rub holes in themselves, also could be the fuel filter.

Maybe replace or test fuel pump, fuel filter, and all internal tank lines with Gates submersible fuel line.

 

What work or maintenance did you do on the bike prior to this trouble?

 

The only thing I remember happening close to when this started is that the bike got a couple flats so it sat close to 2 months before I had them fixed and I put new rear Lyndall Z brake pads on it. I thought maybe the back brakes were dragging causing the bad gas mileage but they seem to be fine. I had the dealer check it out anyways and they too said it seemed fine.

 

Well I got a call from the dealer today and unfortunately it has gone like I expected which is why I waited so long and was reluctant to even drop it off with them.

They said they noticed I had an aftermarket battery in it which they recommend I replace with a genuine Harley battery. Umm no. I told him I have had it checked 4 times now, once from them just the other day and all places say it is fine.
The lady then said I could come pick it up so I asked her if it was fixed and she said she guesses so. I asked her what they did and she said they replaced the spark plugs. I told her I had already replaced them and wasn't going to pay for another set. I asked her what else they did and she said the technician said a connection wasn't tight. I asked her what conneection and did he fix that. She said she didn't know but no, he didn't fix it. I was pissed. If he really did see something loose why didn't the fool fix it instead of just leaving it loose and telling me my bike was fixed?
I asked to speak to the manager and he got on and told me my battery was aftermarket (no ****) I said it was fine and that wasn't the problem because even they said the battery was fine and it would crank fine, just at times the bike wouldn't fire up. I asked him if I bought a new genuine Harley battery and then it did it to me again where it wouldn't start would he refund the battery and he said no so I told him to forget that.
I then told him I already replaced the spark plugs and he asked me if they were genuine Harley plugs and I said yes and I'm not paying for another set since that wasn't the problem.
I asked him about the loose connection and he said he didn't know what it was because the technician didn't say. WTF!
I told him I had already tightened the battery connections well at all 4 places so I know it was not a problem there.
He said it was starting fine for them so he couldn't find a problem. I told him that it was intermittent and would start fine for me too, it just happens at random times usually after it sits a few days. I told him that is exactly why I didn't want to take it in because I was afraid they would start it and then say there wasn't any problem and just push it out the door.

He then asked what pipes I had and if anyone had put a Power Commander or something on it. (I guess they didn't look at the damn bike too well). I told him it has V&H short shots on it and they were the ones that put the Power Commander on it. He said he suggests next time it does it to just unplug the Power Commander and see if it starts. (is it really that easy just unplug it or don't you have to plug something back up in place of it?) so I think he may try to sell me a new power commander.
He said they also tested the charging system (that isn't even it as the damn bike will crank just not fire up and anyways I already checked and it is getting 14v+ while running and sometimes it does the crank and no start coming straight off the charger and the battery read 12.75V this last time it did it).
The only thing they tested that was worth it was the fuel pressure which they said tested out fine.
Anyways I told him I want the bike fixed so I don't want them to just rush it out the door because it started for them the first time. I asked him if he would let it sit then try it again.
He kept trying to tell me they can't fix it if it won't happen while they have it and I do understand that but come on, don't just start the damn thin g once and it starts fine so push it out. Work with it a little at least.
I also reminded him that the mpg had dropped sifgnificantly and he brushed that off and said it was hard to tell why that happened but I tried to get through to him that that might be a symptom of what the problem is which he didn't want to seem to even consider.

I have a damn feeling I just wasted money for them to look at it and I am going to end up replacing parts on my own and until I figure out the damn problem.