It's easy to get to.
1. Take the seat off.
2. Two 10mm bolts underneath rubber caps that hold the rear cowl on, as well as two plastic push-in clips at the front of the cowl, one on each side.
3. Remove the wires connected to the taillight and set the cowl aside.
4. Two bolts on the side of the rear tray (look at the back of the tray, just inside if the exhaust exit points). Take those out.
5. Under the fender, above the hugger, are two more small bolts that hold the bottom of the tray to the frame, take those out.
The whole rear of the tray should move a good 10" at this point, more than plenty of room to play with the ECU and wiring harness.
Oh, and call around to some salvage yards or check ebay. The ECU is one of those units that if it's still in one piece and hasn't gotten wet, it probably still works.
2009 Aprilia Tuono - Ginger
2001 XR650R BRP (Big Red Pig)
2006 Honda 599 - Ex wrecked it :-D
2007 Honda CB900F (sold)
2006 Honda VTX 1300C (sold)