The closest match I have for schematics is a 2000 FLHT, FLTR & FLHR. My schematics show the fuel pump relay supplying power to the coil, both injectors and the fuel pump. Double check your schematics. BAS gets it's power from the ignition fuse & not the fuel pump relay (see entry point # 12). BAS output (to kill engine) goes to pin 7 of ECM.
I can't imagine the Police bike being that different in this area.
Take a look at these two attachments and compare them to what you have. Do you see any dramatic differences from what you have. Especially in the area of ECM power relay, Fuel pump relay, Starter relay. My schematic shows a total of 5 relays. The three I listed plus a Stop light relay & Power relay, so we match there.
I have no reason to doubt you but I want to confirm before we start:
1) Your absolutely positive that the relay you hear chatter is the fuel pump relay.
2) You have no codes. I have never heard of holding the trip button and turning the ignition On/Off 3 times. It sounds like your going into some configuration mode or TSM diagnostics. During normal operation, the check engine light illuminates for approximately four seconds when the ignition is turned ON. The check-engine light then turns off and remains off. If a diagnostic code(s) has been set, the check-engine light turns on for four seconds, turns off, then turns back on for eight seconds or longer.
What happens to your check engine light when you boot the ECM. Does it show a stored code? => (If a diagnostic code(s) has been set, the check-engine light turns on for four seconds, turns off, then turns back on for eight seconds or longer)
3) Are your manuals genuine or aftermarket. I am using aftermarket. Do you you have the ability to scan a page out of your manual and save it as a PDF file?