Bill, thought I'd give an update on my own battle. Maybe it will give you some encouragement.

I also would get pain in the knee when driving and even when sitting sometimes. After my last cycle my knee cap hurt the next day. I went back to the physio and he seemed surprised. He just did some more stretches and some massage on my glut. When I did my quad stretches later at home I would get a quite intense burning sensation just above the knee for the first few stretches. I continued to cycle about 10 miles every second day with very light gearing (no higher than 4th) and didn't feel much pain but the burning sensation remained when stretching.
When I went back to the physio earlier this week I told him about this. He then did some pretty intense massage on this area and up the quad. The pain was almost unbearable. Since then the burning sensation has completely gone and I can stretch pretty well now on my bad leg, almost as good as my other leg. Since then I've been out on two 10 mile cycles and I've pushed it really hard both times and my kneee feels fine. I almost can't believe it. I keep expecting the pain to return but so far it hasn't. I'm optimistic for the first time in ages.

So I suggest you get a thorough check done on your flexibility if you haven't already and if you can pinpoint areas that cause difficulty it might be the answer to getting over this thing.