I removed my tank and fenders to have them painted. Prior to doing this, I pulled out the 40 amp fuse just to make sure the alarm would not sound. The fuse was pulled out for about 3 weeks. 

After putting the fuse back in, my bike is dead. No head light, no horn, nothing. The alarm used to chirp when I turned on the ignition, but now nothing.

So, I tried to remove the fuse again (turn on key, then pull out fuse), but now this causes the alarm to sound. 

Anyone know what is going on?

 

So the fuse hasn't blown? The contacts look clean? The run switch is turned to on? Fob batteries are newish? Battery is charged?

My guess then, you've pinched some wires while putting the tank etc back on...

PIN number? Its a harley we are talking about here, not an ATM...lol...fancy a harley needing a pin number; I'm so glad I have an Evo!

As already mentioned , try the FOB battery(s) first

Easiest and cheapest cure and i've seen this kinda gig LOADSA times