He has a ton of knowledge, comes in handy sometimes.

OP, you can get cycling shoes made for flat pedals, some of them are pretty cheap like at Nashbar, etc. Way better than sneakers.

+1 Big John, you nailed that one. You (OP) might try visiting the 50+ Racing Forum, even if you do not race the knowledge from the members there is really helpful. Hermes and the others have always encouraged me in my riding and regaining my health. Good folks, all.

Bill

Hermes, thanks for you help and insight. You said about the videos about what I figured.

Customizing it is half the fun. I am staying with a mountain bike because I want to be able to go any where with it. Fortunately I don't have to have every thing done in one day. I am looking to having it finished by next spring since i just got the bike and back into cycling this summer. I have been getting as much advice here and locally as I can.

I have been scouring the web for exercises and stretches, thanks JanMM, I will have to try that.

Here are three good, quick exercises. I am already doing some thing similar to the third one, https://www.youtube.com/watch?v=FWvNxZrgK1w .

I bought an extra long (350 mm, they didn't have 300 mm) seat post because the on that came with the bike was a little too short and I had too much bend in the knees. I tried it today and it work very good, makes all the difference. I feel like I'm sitting 10 feet in the air though and am going to hit my head on every branch on the trails.
I have been wearing shorts (not bicycle shorts) this summer while riding except for a couple of times. The two times I wore long pants the weight/pressure from the pant leg would make the left side of my left knee cap hurt enough that I had to stop riding. The first time was before I started stretching and strengthening and it started hurting quickly. The second was after I started stretching and strengtheningand it took quite a bit longer. Today I wore long pants because it was cool outside and with the new taller seatpost there was no pain. I noticed that there was almost no pressure on my knee from the pants because my leg was straighter. I took a padded, slip-on knee support with me and was going to wear it but I figured I would the seatpost a shot first. I am getting this bike, my knees and my riding technique dialed in.