I have a very similar sounding issue which arose while I was cycling to and from work during the olympics.
I had started cycling to avoid the traffic in London, this meant I had gone from 0 miles to 32 miles a day.
I hadn’t done a lot of road riding at this stage and my experience of riding techniques was poor, i figured to go faster you keep cranking up the resistance.
I was pushing a harder gear than normal and this is what did the damage.
If you are not already, always try to keep your cadence high in an easier gear.
Ensure your seat position is the best it can be, cycle slowly around and have someone take a photo of you side on to get an idea of where you are situated on the bike.
Too low a saddle
Too high a saddle
Saddle too far back
Saddle too far forward
Stem too long
Stem too short
Stem too high
Stem too low
These can all contribute to putting additional strain on your knees etc.
There are lots of articles on bike fit which you can either try to measure up accurately or try to mimic in your own way.
Through changing my riding style and fitting my bike to me I have considerably reduced the amount this issue affects me.
I can comfortably do a 50-60mile ride. I did the Ride 100 and that hurt but a lot of that was due to me crawling up hills alongside my partner who is a pedal masher!
Summary
Pedal mash bad.