Yup, I've read the sticky and just about most of the anchoring threads on the site.

I used to anchor till the day before, but then I came across many posts on UG which said how anchoring creates tension, leads to CT, blah.
So I decided to stop, and practiced not anchoring all of yesterday, and it seems to be working well - I can pretty much play the same stuff now, although with a slight loss in accuracy (nothing which a few days of good practice can't work out, I'm sure).

So my question is :

I read in the sticky
"My arm touches the guitar! - That's okay."

Thats exactly what I do. My wrist is free to move, though.

When I seperate my arm from the body of the guitar, my shoulder starts to ache a lot after just a few minutes of playing.

So firstly, is the arm touching the guitar anchoring? (if its not, then I plan to keep playing that way).

And secondly, if it is, will the pains in my shoulder go away with time or do I need to work on my shoulder strength and do specific exercises?

As Freepower said in his sticky, if your arm touches the guitar that is fine no problems, ask yourself do you need to keep your arm in that one spot to be able to play? If so you are anchoring and need to try to follow Freepowers advice to rid yourself of it.

I can move my arm around and still play the same stuff, but when I totally remove my arm from the guitar, then my accuracy goes down and my shoulder gets strained a bit.

Is that anchoring?

My situation is exactly like Mr. Vai here :

I believe his forearm is touching the guitar a bit, but his wrist is free to move.
^ yeah, that's cool. Here's the most likely solution, I've edited in an extra sentence here and in the sticky.

Don't just lift your hand up an inch. That's simply bad posture and will damage your playing - people who complain of elbow or shoulder pains after unanchoring are generally doing something like this. All you need to do is lift your hand a millimeter or two, gently curl your fingers in, and you shold have left all contact with the guitar. That's the kind of position we're talking about.