I get more knee problems when I use higher gears. It seems like I avoid knee problems when I use higher RPM's and lower gears.
This also seems to fatigue me less and doesn't hurt my speed at all.

I try to consider my legs as I would a small engine: higher RPM's,
rather than more cubic inches (or CC's,) to produce more power.
I think my knees can handle fast spinning better than they can strong pressure.

Also, I take it easy for the first 5 or 10 minutes of my ride to warm up. All this "advice" is in addition to what others have said.