Storing 2006 HD 1200 XL Custom for the winter. I have it hooked up to battery tender. Periodically I will take it off the tender when indicator light turns green, indicating battery is fully charged. Will plug tender back in 1-2 days later. Indicator light is now red, indicating charge is needed. Is this typical ?

I all your worried about is the battery, get your self a battery tender to hook up when it is in storage rather then disabling the alarm system.

Sound like you need a new battery
Lee2007xl1220c

Harley Davidson Wiring Diagrams and Schematics

Get one of the smart chargers made by Battery Tender or Yuasa. You can get one of those that look like the power supplies for telephones, "wall warts". or you can get multiple units that charge up to six batteries. They come with "pig tail" wires to permanently connect to your battery making it easy to connect up the charge when you get finished riding. They keep you battery fully charged, extend the life of the battery, and won't overcharge it even leaving it connected continously.

Good Luck
Steve

Most people use what is called a Battery tender... which is just a fancy way of saying low amp (2Amp) battery charger...
Buy one , and hook up the quick connect harness provided... plug it in... and you are good to go... It is said that use of this battery tender system extends the life of the battery by as much as 100% ( double the life expectency !!).

so , dont remove it... Tend it...
For storing your bike in an are without electrical outlets... use the solar battery tender !

bike cold and on jiffy stand with 10 pds of force for the xL883 c/xL 1200 c/xL 1200 L 1/4-5/16 in for the xL883xL 883r 1200 r/xL 50 9/16-5/8 in

Sounds like a dead battery to me. Hook it up to a good charger not a battery tender.

you need to change your rectifier this is a common fault with harleys