You've gotten a lot of good advice here already. I would second the suggestion to slow down your cadence if you're doing a lot of super fast spinning and focusing on movement control through the pedal stroke.
Over extending the knee can be the cause of knee pit pain as you call it. I love that phrase by the way. But that doesn't just come from saddle height, it also comes from not controlling the motion through the pedal stroke.
The tissues that often cause pain in the back of the knee are the popliteus (in fact the anatomical name for this area is the popliteal fossa), gastrocnemius and hamstrings. I very commonly see people with popliteal irritation from cycling. Often it's from incorrect cleat position in terms of rotation, so if you're clipped in, that's another thing to think about.
Living life like there's no tomorrow.
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2007 Look Dura Ace
2010 Custom Tonic cross with discs, SRAM
2012 Moots YBB 2 x 10 Shimano XTR
2014 Soma B-Side SS