I'll keep my comments strictly to the SS part of what you're doing as that's where my experience is. First question: do you own Starting Strength: Basic Barbell Training and/or Practical Programming? Doesn't matter to me if you do, but if not, both contain much more info that you will find on the web about them.
Particularly PP, as it will lay out your plan for after the novice program also. I'm also a believer that if we are to use Mark Rippetoe's knowledge to improve ourselves the courteous thing to do would be to buy one of his books.
Anyway... Rip's method of squatting is to use a low bar-medium stance, you are doing this?
Even though it was lighter than you want, this actually implies that you started too heavy. Drop down until you have perfect form, as that will be very important when you get to the heavier weights. Also use all of your warm-up sets every day to constantly work on perfecting your form. Don't worry about starting lighter as you can jump 10 lbs per workout until that begins to get too heavy, then 5lbs, so you can go up over 30lbs a week for a couple weeks if you can handle it.
I would not do 3 sets of deads. Rip has some very specific reasons for doing 1 set. This stuff isn't rocket science and there is room for changes, but at least in my case Rip knows more about it than I do and you should definitely try to follow the program exactly at least for a little while.
Leg press is a different animal and has little correlation to your squatting strength. Oftentimes, we blame inflexibility or core strength but the real issues is your stance. Medium stance, toes out, knees out hard. The physiological reasons for this are in the book.
This usually is not a shoulder or wrist problem, but actually a problem with bar placement. Are you confident that you have the proper low bar position, and not high bar or something in between?
Sorry for the long post. I'm not the expert as I'm still going through the program also, but I have had some of the same issues as you. Feel free to take everything I wrote with a grain of salt or disregard completely.