I have wanted to get a true campaign up and running for some time now but player and time restrictions keep coming up. I did find this set of rules you may like. [url]http://www.scribd.com/doc/39219328/Planetary-Empires[/url] I like this rule set for the character advancement. It allows your heroes to grow each game. I played a test run of the rules and they can be easily exploited so I recommend not following them literally. (The tyranid player ended up having 30%+ more points worth of units than his opponents after he acquired a couple manufactorums). My latest creation would be to combine the character advancement from the link above with the rules and victory point system from the crusade of fire supplement.
Look into that and let me know if that helps any.