I am missing parts.

If your'e referring to the back up battery in the alarm itself.
I have a 2012 Fat Boy, and my alarm is not a Harley item, but is mounted in the stock Harley location. It is between the rear wheel mud guard and the battery box. The rear wheel must be loosened, and lowered or removed, then the mud guard loosened or removed. You can see some of my alarm when looking at the bike from the clutch handle side, just behind the battery location. Some parts might be apparent there, but not accessable unless you do the above. I had mine professionally installed cause the rear tire looked like a task I'd rather pay for to have removed. I needed a new tire anyway, so the overall service cost was lower having them both done at the same time.
PS Harley will not install an alarm that's not a Harley brand.
I hope this helps. Good luck

No, you can charge it in place.

In fact, a "battery tender" is a good idea:

http://www.ebay.com/itm/BATTERY-TENDER-12-Volt-Trickle-Charger-CAR-BOAT-ATV-12V-Junior-Jr-Motorcycle-/231110566640?pt=Motors_Car_Truck_Parts_Accessories&hash=item35cf4362f0&vxp=mtr

The "pig-tail" on the right of the pic is installed to the battery posts, the the charger plugs into the other end that you have mounted remotely in an accessible area.

Hi, Anonymous 12 volts, for this scenario you will need your service manual that has all fastener torque specs -fluid capacities and a wiring diagram on the back pages, parts fiche, and owners manual if you can not find the best tool you ever bought for your Harley, despair not, for a mere zero $0 you can download another one.
For more information about your issue and valuable "FREE" downloads that you will need for viewing or printing please click on the blue links below and for more specific information or questions at no charge please feel free to contact me at [email protected]. Good luck and have a wonderful day.
https://www.totalmotorcycle.com/photos/2004models/2004-Harley-Davidson-FLSTFIFatBoy/
http://www.mediafire.com/file/65o6mbkdq5ty8ke/99_to_05_Harley_Softail_Service_Manual.pdf/file
https://partsfinder.onlinemicrofiche.com/ronnies/showmodel.asp?make=hdmc
https://serviceinfo.harley-davidson.com/sip/service/document/6300
https://www.6ya.com/ to speak to me personally

Hi, Mark for this scenario you will need your service manual that has all fastener torque specs -fluid capacities and a wiring diagram on the back pages, parts fiche, and owners manual if you can not find the best tool you ever bought for your Harley, despair not, for a mere zero $0 you can download another one.
For more information about your issue and valuable "FREE" downloads that you will need for viewing or printing please click on the blue links below and for more specific information or questions at no charge please feel free to contact me at [email protected]. Good luck and have a wonderful day.
https://www.harley-davidson.com/us/en/shop/c/motorcycle-parts/2005-softail-fat-boy-flstf?format=json;i=1;locale=en_US;q1=parts;q2=motorcycle-parts;sp_cs=UTF-8;x1=primaryCategoryCode;x2=superCategoryCodes;fitmentFilter=2005-FLSTF
http://www.mediafire.com/file/65o6mbkdq5ty8ke/99_to_05_Harley_Softail_Service_Manual.pdf/file
https://partsfinder.onlinemicrofiche.com/ronnies/showmodel.asp?make=hdmc
https://ownersmanuals2.com/harley-davidson/fat-boy-2005-owners-manual-66398
https://www.6ya.com/ to speak to me personally

Sale me transmitter of HD