I've been dealing with a knee issue since June and there are a few reasons. One of them being fit incorrectly by a guy from a bike shop.(My pedal and shoes were off, seat too low, and too far back, handle bars too low, all contributing to my knee injury- and not knowing when to stop)The other being not giving enough time off the bike to let it heal on its own. Try to let your knee heal completely because each time it's reinjured it takes longer to heal and more damage maybe done.
As for having the bike guy help you-if you feel he is really knowledgable then I would go to him. Or maybe the shop can recommend someone. I am spending a few extra bucks to have a professional cyclist and coach by the name of John Howard, help me with adjusting the bike to me and my needs. He does this for a living. So maybe you have someone in your neck of the woods who can do the same.
If the adjuustments don't work than give your bike guy feedback so he can help you.
Good luck!
P.S. It doesn't matter if you ride fast or slow-5 miles or 100 miles, a good fit is important.