I was doing some work on my 08 Ultra today which involved disconnecting the battery, I put the bike in Transportation Mode thinking it wouldn't alarm when I unhooked the battery, I was wrong. I've heard the could be put in a Maintenance Mode which I think prevents the alarm system for going off even if the battery's disconnected. Does anyone know how to do this ?

 

There isn't a plug on the siren, or will it sound off if the plug is pulled? The owner's manual should fill in the details.

 

With fob present, turn ignition on, this will disable the alarm. You can then pull the maxi fuse or the battery.
Transportation mode only disables the motion sensor.
There is a service mode that allows you to leave the bike at a dealer for service and you can take key/fob with you. I thought dealer did that using digital technician, but could be mistaken.