Was lucky to make it home from Sturgis this year back to So. Cal.
While in SD the 40 amp fuse in my 06 ultra classic failed. Got on line and discoverd that replacing it with a 50 amp fuse has helped in many cases.
  Lasted me the rest of the trip and all the way home. Recently had a few time where the bike wanted to die when coming to a stop. On a few occasions it did die. Shut everthing off, turned it back on and was good to go. Yesterday the 50 amp fuse fails when attemting to start the bike. Installed the spare I had with me and the power came back on but when I went to hit the start button,... nothing. Didn't blow the fuse right away but If I hit the start button repeatedly, it would blow the fuse again.
 This just happened last night so I haven't had the chance to dive into it yet, just thought I would see if anyone has experience with this problem and how it fixed.

   Thanks
    Alter Ego

Dont know about the fuse. but my 06 ultra shuts down at idle or going down the road. I turn off switch and back on, push start or pop clutch and starts again, been doing this for two years, I have no idia and HD dealer cant find the problem in thier diagnostic machine. So i guees this 50 amp fuse has not fixed your problem? Someone said ignition relay ( module ?) My manuals do not mention a ignition relay.

Yea, the 50 amp fuse turned out to only be a temp fix. Gonna dive into it this wekend and see if I can find something.

Thanks Rex, I'll follow your advise and see if that helps. Just starting to break it down now.

Well, pulled the battery and disconected the starter. Inspected all the wires. Found nothing obvious.
So cleaned all the terminals and conections and put it all back together.
Plugged in another 50 amp fuse and it fired right up. The connections didn't look bad at all, but cleaned because I had it apart already. Tomorrow I'll go pick up a 40 amp and see if it holds up If it does I'll just carry some extras with me, both 40's and 50's.

Thanks Rex
I'll keep you posted
ALter Ego

I'm rolling with Rex on this, about be careful not to over fuse (only in emergency). What ever cause the 40 amp to blow could cause other problems, becuase it will take a bit longer to blow a 50 amp fuse. Like Rex how did I know that???

sounds like an intermittent short to ground, when you hit the start button, feel around on what wires are exposed, if one is getting warm to touch or hot, there is a short, and you can follow that wire to the source of the issue. or at least tell the tech which wire it is. shorts won't show up on electronic diagnostics. only physical diagnostics find them typically. what circuit is the fuse in? charging?, starting?

Update.
Picked up a 40 amp fuse this morning, pulled the 50 amp and installed the 40. Bike fired up no problem.
Shut it down, fired it up, shut it down, fired it up. So it looks like just cleaning the connections at the battery and at the starter has solved the problem even though there wasn't any corrosion. Just what looked like a what I can only describe as a little film. So I'll run the 40 and carry an extra 40 and 50 amp fuse.

Bad, seems to be the starting circut. The volt meeter was reading a consistant 14 range.

Thanks for the input from all of you

when you engaged the starter, what did the voltmeter drop to?

The voltmeter would drop to about 10 when I engaged the starter.

Something to keep in mind, the nominal current draw on most bikes is about 25 amps. That takes care of the lights and for all of you big glide riders any radio, gps and like us up north heated clothing. The 40 amp rating is to absorb the spikes that are associated with starting. Now from what you have described here, you have a wire that is momentarily touching the frame, or a wire that is being rubbed bare. You must be very observant when the bike shorts out. Something in the structure of the bike is stressed out of position and makes this wire short out. Over fusing can do a couple of things to you and for you. The obvious is that it can get you home, the not so obvious is that it can allow so much damage to occur that you will find the problem. The damage up to and including a fire. Someone well versed in basic bike electronics is what you need, cause finding this will take time and skill. In the mean time, do not for any reason over fuse. Carry a pocket full of 40 amp fuses to get you home.