I don't know about the specifics of analyzing radio waves to search for intelligible communication, but I can suggest one thing. The Kepler telescope set out to hunt for earth-like planets that may contain life. The SETI project as far as I can tell is scanning every part of the sky without discrimination. I suggest that Kepler and SETI team up so that when Kepler finds a planet that is capable of supporting intelligent life, SETI will point its telescopes to it and then run whatever algorithms you have to analyze the radio signals if there are any from that planet. This current method of scanning arbitrary locations in the sky sounds like it could be wasted effort when you don't know what it is you are pointing the radio telescopes at.
