Sadly, it IS a complete *****, and there are NO shortcuts or tricks.
The ignition is basically held there by a one-time-use "anti-theft" bolt that, by design, has it's bolt head sheared off during installation. The remaining bolt shaft is filed down to the dull circular point you see when you turn the triple-tree upside down.
To separate the two components, the bolt has to be drilled out. There is no other way to remove your ignition assembly from your broken triple tree. Sorry, 'bro, but that's the way it is....
If you experience no joy with a warranty claim, do note that there are other triple-tree options available for the FJR. This might end up being important to you, as the upper triple tree retails for wall over $100.00, and is currently on backorder; there are none in the Yamaha Supply system as of this writing.