I have the exact same dies for my 7mmRM and they scratch the brass just the same as you are describing. My scratches are not running the length of the brass (from the case head to shoulder direction) they are running around the case body. They are very light scratches and when I put the cases back into the tumbler to get all of the lube off of them they are generally all gone. I don't know if this is a problem of any kind for us, but I can tell you I do see the same thing.
As far as your decapping pin goes, mine is the same as well. I feel like I have a ton of decapping pin sticking out the base of my die, but that's just how it is I think. I can tell you from some experience that you want that expander ball aligned with the vent hole as described in the instructions that came with the die. How do I know? I have to laugh to myself as typing this. Let me see if I can post you a link to a thread I started just a week or so ago. Here it is:
What is my problem? Pic inside.
As far as the amount of effort that I have to put into sizing, I can't really say that I have had that problem but once, and that was when I wasn't using enough lube. At the time I was just using some lube on a lube pad, and I was getting into really having to put some pressure on the brass. I then stuck a case, so watch out. If you are putting that much force on the brass then I would back off and bring the ram down, size a little more until it gets tough to push, then bring the ram back down until you have the whole thing sized.
I don't know if I am making sense, but instead of trying to size the whole piece of brass with one stroke of the ram, size a little at a time bringing the ram up and down until you make it all the way to the shell holder. If you're not careful, you will do like I did and put too much elbow grease on it and end up with a stuck case and when you try to bring the ram back down the shell holder will just pull through the rim.
So after all of that, I would say make sure you are getting the sizing wax all over that case as well as inside the case neck to help the expander ball out and you should see it get much easier to size those. Hope my rambling helped some.