First, congrats! Mooney is really among my favorite builders, and I love his attention to detail. He also tends to pick really good painters, which makes a lot of difference. Please take more photos - the head badge, close ups, etc.

So the stem question...I've always changed them because of their rep, but don't have direct experience. There is some rumor mongering and exaggeration when it comes to some parts being problematic, but I don't know if this is such an example. That said, this bike deserves a Cinelli, or 3ttt, stem regardless.

On the brake track - this happens. If it still stops and has machining, I wouldn't worry about it. If not, replace the rims. I don't think you can really restore wear to a worn rim.