my worst enemy

[KnottedYet]

No luck with finding a shorter crank so I will give my LBS a call and see if they have a gently used part that I can try. I also found out that I do have "severe chondromalacia" per the doc's diagnosis. I guess then I probably won't be able to ride relatively pain free on the bike then? Even with quad/hamstring/glut exercises?

Chondromalacia is always a symptom of something else.

Something is out of whack with your body mechanics or posture or habits, and that causes the cartilage on the back of your kneecap to get wolloped.

Just like having sores in your mouth is a symptom of something else (say, eating sharp tortilla chips) which will go away if you fix the cause (taking smaller bites of chip and chewing more carefully); so is chondromalacia.

Randomly strengthening leg muscles isn't guaranteed to fix your mechanical problem. (what if your chondromalacia is caused by excess tibial torsion from an overly-strong medial hamstring? Strengthening your hammie won't help then!) Ask the doc to figure out what caused the chondromalacia in the first place, then work with a PT or trainer or whatever to address the actual cause of the problem, it will be much less frustrating that way.

If your medial weightbearing surface of the knee is truly "gone", then you are a candidate for replacement. Perhaps a hemiarthroplasty would be appropriate. Depending on the issue, synvisc might be appropriate. There are a lot of options, but first ask just what he means by "gone." There are lots of folks running around on bone-on-bone knees, so leaving it alone and working on proper mechanics and supportive muscles might be an option, too.

Whatever imbalance or mechanical problem caused the damage to the medial surfaces is probably the same thing that is causing the chewing up the backside of the kneecap. Two birds with one stone if you can narrow it down!

(and if your doc didn't actually look at you on the longer cranks on your particular bike, I'm not sure I'd take his word that the longer cranks are fine.)