1. Correct.
2. Incorrect. Think about it. Thicker string in the slots won't make the slots deeper. Well, maybe eventually, though I doubt it.
3- The jury will be out on that until the cows, and maybe even Mister Quackers, come home. I wouldn't raise the stopbar here, I know that much. You could lower the bridge if it bothers you. Don't think you have to do either.
The pickups appear to be set pretty high, esp. the bridge pickup, so lots of room for experimenting. Just remember to write down the starting points. 490s usually sound good to my ears in an SG, and from that pic alone I can tell you can adjust things quite a bit.
It's New Gibson Syndrome. Take a deep breath. It's gonna be fine.