I did the jumper mod, PCIII and an Akra slip-on to my 06 636 and the answer is YES it works. I dyno'd the bike with the different mods added one at a time and the jumper mod allowed the engine to hold it's max power all the way to the rev limiter. I've read that the jumper mod on the 07 is the same deal as the 06 so you should have the same results.
There's no reason not to keep the jumper mod in place after upgrading exhausts. There is some controversy on where or not it helps but I think in general people say it still makes a difference (even though the major thing it does is keep the exhaust valve from closing back down due to noise regulations above 12,000 RPM with the stock exhaust).