First - Thanks for all the input. I think I will try to see a PT soon and see how that turns out.
Sorry for the late response - Very busy weekend - To answer a few questions:
I am a very fit 46 year old. Im around 6'1 and 185 or so. My job has me sitting in front of a computer or sitting in a drivers seat, so I probably do not walk enough, but I do stay very active when I am not working.
I have tried different shoes - when its cold, I generally hike in a pair of Solomon Hiking boots and during warm weather I will hike in InoV8 Trail Runners. Both seem to fit well and are not very old.
My pack is fairly light. Around 12 lbs base weight - add in Water and Food for 3 days and its around 20. I use two hiking poles and I sleep in a Blackbird Hammock (dont sleep very well on the ground)
I spoke to a Dr. friend, who lives in the same neighborhood as me and He has offered the same advice. See a PT - More than likely after a few weeks on trail my muscles and joints will adjust to the walking and will probably get better.