A unicycle is unique, unlike a bicycle where you can change gears, coast, and rest your legs, unicyclists are forced to use their legs to stop, balance, and pedal in time with their wheel speed.
First off, knee pain comes from over use, whether from pedaling too much, pedaling too hard, having too much knee angle, whatever your problem it is still from over use even if it is misuse
Since you are already doing physical “rehab”, which I assume includes stretching and cross training, lets focus on the mechanical side of the work your legs are doing.
There are a number of ways to reduce the work your legs/knees are doing:
Shorten the cranks (reduce knee angle)
Ride a larger wheel (reduced rotations/cadence)
Ride Slower (reduced speed of rotation/cadence)
Ride easier terrain (obviously this will be easier on your legs)
Lengthen your legs by raising the seat (improved efficiency/reduce knee angle)
For each of these changes there is a downside:
Shorten the cranks = less leverage for climbing, braking, and control
Ride a larger wheel = requires more effort to start, stop, and maintain momentum
Ride Slower or easier terrain = Not as fun…
Lengthen your legs by raising the seat = less seat clearance for out of seat climbing and obstacle negotiation (muni)
Also consider the possibility that you are exceeding your body’s ability to recover and or your not yet in shape to ride as you would like to ride. In my experience, when you embark on a new sport, esp one that requires a new set of muscle development, it takes years to develop muscle and bone structure to support the demands of that use, esp if you are trying to do that sport at your limits.
Also, because unicycling requires the user to maintain balance at the same time they are maintaining propulsion, experience and time in the seat can make a huge difference as to your efficency and endurance. So the better you are at riding, the less work you do when riding.
I have played with crank lengths, shorter did not help my knee pain, in fact my knees hurt more because I was working harder on climbs and descents. As a result I tend to run longer cranks (165s) when I am going to be doing extreme ups and downs, then shorter cranks when I am going to be doing more flats. I also use brakes which take the pressure off my legs on downhills.
=> And after all my long winded verbage, this single comment is what catches my eye:
You need to look at the most obvious issue: You are a new rider, you have not developed the balance and physical structures to support this activity, as a result you are suffering from overuse.
Shorter cranks will not replace experience.
Ride easier terrain, emphasize time on the seat, give yourself a rest day (or two) between rides, use NSAIDs, get a brake if you do downhills.