I have the same bike. I put my flasher (a BackOFF XP) under the seat and under the ignition module. There's enough room to push the tank connector over and stick the flasher directly to the frame. As long as your RearAlert model is roughly the same size, it should fit.
Also, when I hooked mine up, I used a two position flat connector in the brake light line. I bought a second connector and joined the two terminals together (like a "jumper") Now, if the flasher module should fail, I can simply take it out of service and bypass it, right on the side of the road if necessary, using nothing more than the bike's toolkit.
It's not that I don't trust the electronics...I just don't trust the electronics...