i personally don't believe clipless pedals cause knee problems.its more likely to be your set up/postion or even cheap shoes
Absolutely the best advice I can give you regarding wheels is find a good wheel builder and get some hand-made hoops. The pair I got cost £400 in bits and another 100 spot for labour, give or take. What I got was a bomb-proof pair of wheels that weigh 1300grams for the pair. You won't get a better set of factory made wheels with the same spec for less than a grand.As regards cheap, light carbon bits like tri-bars, planet X are normally the boys.
I got a pair of new wheels on order from them. Mavic reflex tubular rims, Tune hubs, x-ray spokes, handbuilt. So on that note I will shortly be flogging my Ksyrium SL's (shimano free-hub) if anyone is in the market for a nice stiff, light pair of clinchers. Me - I'm going fully old-school with tubs again