Knee trouble can have many sources, depending on the type and location of pain. Your pedals may not be the culprit.
• Get your fit checked by a professional.
• Minimize the amount of gear you carry.
• Make sure to use a high cadence at all times.
• Do a couple of weekend tours to shake out your gear.
As to pedals, IMO clipless isn't nearly as important for touring as people presume. It's a myth that you genuinely "pull up" on the pedals in a truly useful fashion -- all you're doing is getting your leg out of the way. If you prefer clipless though, you may want to adjust your fit before changing the pedals.