Here's my 0.03 (I've already chipped in my 0.02!)...
From looking at the wiring diagram and doing a bit of research on electronic flasher relay units here's what seems most logical, assuming the three contacts on the electronic flasher relay are: +12v, GND and switched +12v out.
I think the controller makes the GND connection for the electronic relay when it receives a demand from the handlebar switch to enable either signal pair. The relay then has 12v across it and begins to operate sending out the pulsed 12v on the Lbl wire back to the handlebar switch. It's at the handlebar switch the correct lamp pair are fed with the pulsed 12v on the Lbl wire.
If all this guess work is correct, the self cancel feature should not be impacted at all by the installation of LED signals. As you're well aware, the problem with LED signals is one of loading on the relay output side of things, not the control of whether the relay is enabled or not - that's the job (and only job) of the controller unit.
I'll be figuring this out for my own reasons before too long so I'll try and do a little digging on my 1100 this weekend, that has the same set up. If so, I'll post what I find but having said all that, I still haven't actually tried what you're proposing.
For reference, I believe the wires to be used as follows...
on the relay:
O/G - +12v
B/Bl - GND
Lbl - switched +12v out (pulsed to make the signals flash)
on the controller:
O/G - +12v
Bl/R - speed sensor
B/R - speed sensor
Lg/B - signal request input from switch
B/Bl - switched GND to relay
Br/Y - Cancel input from switch
B/W - GND
Hope this sheds a little more light - no pun intended of course!
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