Don't have a problem with spd's but when my mileage went up big time on the road bike this year I started to get a right knee problem (LOOK Keo). I noticed that on spd that as well as my R ankle being turned in a lot, which I had set my Look cleats to mimic, that my foot also pronates a LOT. By this I mean that the outside of my foot is lower than the inside. The small platform of spd allows this foot rotation but the bigger and more fixed platform of the Keo's holds the foot much flatter. So I added both wedges in to my Spesh road shoes (which I think gives +3 degrees). Since then no pain. I can still "feel" something in the knee, a little stretch maybe, so maybe more adjustment is needed but I can't afford custom footbeds. As the pain as gone I feel that the majority of adjustment has been made.
I recommend that you have a go. Be prepared to adjust/add/subtract as you go. Also remember that a change may not feel right straight off. Stick with it but not if you definately feel that there is something wrong.