I can't get it 100% clean either, but an overnight soak in oxyclean and a blast with my high pressure hose nozzle works well enough, IMO. The nozzle I speak of is one of those little metal pointy ones that are not adjustable, with a very small orifice to create quite a high pressure. After the soak/spray method, there's no way that anything I missed will affect the taste of future brews.
For the siphoning problems, here are some hints from Dennis (the creator of the Hop Stopper):
"Regarding the loss of the siphon. When using a pump, the outflow of the wort from the kettle can exceed the wort's ability to flow into the screen cavity. As soon as the top of the screen is exposed to the air, air can be drawn into the screen cavity. Eventually, the screen cavity will empty out even though the kettle isn't empty and the siphon will be lost. As Kal mentioned, when using a pump, it is advisable to slow down the flow of wort toward the end of draining. If you notice any bubbles leaving the kettle, that means the siphon is getting ready to break. If this happens, immediately shut off the flow at the pump outlet. Leave it closed off for 10 seconds or so - this will allow wort to refill the screen cavity. Then slowly open the pump valve to allow flow again. You will likely have to finish draining the kettle at a reduced flow rate in order to maintain the siphon until the kettle is empty. It is typically the combination of break material and hops that restricts flow through the screen. When using a counterflow or plate chiller, there isn't any cold break, but there is still hot break and other proteins from the malt.
It's actually beneficial that the pick up tube is not in the center of the kettle. The center is where most of the debris gathers. Regarding the seal, as long as you can siphon out water with no breaks in the siphon, then the seal is intact. I am nearly positive that the problem you experienced is a result of pumping out the wort faster than the wort can flow into the screen cavity. If you follow the advice above, I'm sure this will solve your issue."