I miss anything? Something wrong, anything right? Any advice?
You're not deadlifting. It would probably be a good idea to deadlift as often as your squat with similar volume. If you are doing 9 sets of quads, then do 9 sets of hamstrings.
If you think you need more fats, then add some olive oil to your veggies.
If you are questioning yourself this much, why not choose a training template from this website. I think TC talked about the Push/Pull in a recent article. There are also many others to choose from.
If you don't know if you are getting the right amount of calories, then you need to count them, and then adjust.
I doubt you have "bad joints". Since you are new to lifting, the last thing probably on your mind is flexibility. You most likely have poor movement patterns due to a lack of mobility. Search 'foam rolling' and get Robertson's Warm-up CD along with Magnificent Mobility. They are worth the money compared to surgery.
You are in the right direction by going towards more of a "phsique" type lifting rep ranges. This will help you learn the exercises properly. If you have anyone that knows what they are doing ask them. Most guys are willing to help.
Forget about weight. After I tore my meniscus I started squatting with the bar. Embarrassing? Yes. But worry about what your body can handle, not your ego.
Lastly, ask Cressey about your shoulder problem. He can help you more than anybody else on here with shoulders.