Knees are sore

Well my knees have been sore from Monday's jog walk routine. I used to run when I was younger and the last time I tried to lose weight. Well the last time I ran consistently my ankle started having issues. I have weak joints especially in my knees and ankles. I really don't think I will continue with the running . I have an appt with the doctor on Tuesday to have it reevaluated. Anyways I can walk for days normally, and usually do about 2.5-3 miles daily with my dog. I have also started a power walking with incline routine on the treadmill for 3 days a week. I did my routine today and I am much better. Not as sore as I was on Monday, but still got a good workout. Burned roughly 500- 600 calories today. Now my question is the power walking better for my knees as I know jogging is wreaking havoc on them and I don't want to be put ou of commission like last time. I popped an aleve this morning before working out and put my knee brace on and did really good. I did bump the intensity down once as I felt a slight twinge but other than that I'm ok. I believe my doc said last time that I have chondromalacia. All my joints kinda suck from being active when I was in high school and having a hard physical lifting job for so long. I am only 33 so I don't want this to reall limit me, but I don't want to get worse. I was lifting some weights yesterday and doing great. (I've always been pretty strong) but wheni got to the military press (I think that is what it is called) with the dumbells at shoulder height and going up, every time my right shoulder would crack. Not hurt, but make a popping noise. It is an old horseback riding injury and sometimes flares up. Is there any weight exercises for the deltoids that won't aggravate my shoulder? I am doing all the bicep and tricep exercises but shoulder ones are bothering me. These are all things I will mention to the doc, but thought I'd ask here as well. I am too young to be all crackly lol!