Always had painful right knee, but usually only comes on during the later part of a long all day ride. Changed to shimano from eggies and today same pain after just under 2 hours? Are Time supposed to be good for knees? Or should I just play around with cleat position ( doing) and insoles( about to)?

play with your cleats, sometimes they feel right when you first get on the bike but they are not, you can normally tell after 5 or 10minutes riding if they are not spot on so I always do a test ride before venturing out.