for what it's worth, some people think to remove an alarm that it's just one more thing that can strand them far from home, and don't believe in them anyway. Personally i put pagers with proximity sensors in for when i'm touring and go into a restaurant with the bike fully loaded.

 

I have a 2001 Fatboy with similar problem.Had tank off replacing bars,blinkers and cables now when you turn ignition on the blinkers flash 6 times and fuel pump doest run. i dont have factory fobs and previous owner says he dont know if it has alarm or not

 

Couldn't you just put it in service mode and remove the batteries from the FOB, then it won't ever reset.. Or on your birthday change you batteries...

 

mine turned out not to be alarm.Connector on right side under tank wasnt plugged all the way in. Back up and running!

 

Took all of 5 min to figure it out. I will give you the RAW details, I do not want to be responsible for any thefts!

You need a stock TSM to start. Disable alarm system, you need the key (not by using the blinker switches). Remove the alarm components (antenna, siren, etc) and install the stock TSM.
Re-enable the bike, done!

The alarm system has a capacitor that will power the alarm system when you disconnect the battery. That is why there is no battery in the alarm system to change other than the FOBs and the alarm goes off without power. It also will continue to disable the bike.

Now the million dollar question is; Will the dealership sell you a stock TSM?

Just my 2 cents!