Your post is all over the place... hardly know where to start...
a) If your actual spine is hurting then you have some serious problems and you should discontinue training until you see a doctor and a coach because you're going to mess yourself up. More likely it's your spinal erector muscles you're feeling. Do the drill in the "low back" platform video linked from the Resources section. Is that the feeling you're feeling ? If so it's fine to feel some of that though it doesn't tell you if you have good or bad form.
b) How do you know you have good form ? have you taken a video ? having significant back rounding as you claim is itself bad form if in fact you have it. Further, having pain in 3 of the 4 joints involved in the squat is suggestive that you may in fact not have great form.
c) In the beginning everything's going to hurt somewhat. Actually if you're working hard a lot of things are going to hurt somewhat a lot of the time. It's a range that starts at benign soreness then goes to things that are more inflamed then they should be but are fine to seriously injury. How old are you ? What is your sports and training background? Where are your lifts? How long have you been doing this? When did the pain start?
d) shoulders and the bench: what about your shoulder did you hurt 3 months ago ? how much weight were you using ?
my basic catchall feedback at this point (as a random internet guy) without knowing more is that you should 1) double check your form, 2) do some lighter weight higher rep sets of the exercises to get things loosened up and "grooved" and 3) if you figure out what's particularly tight or weak hit up mobilitywod and find a couple of appropriate drills to do for those parts.