I'm not at the house right now, and I don't remember what size the copper pipe was It was slightly larger than the beer out line (just bring a piece of line with you to the store and check). You can buy the copper at HD or Lowes for $2-$4. I bought precut 2' pieces and cut them down because I though I might be able to get away without having to cut them. The copper is held in there by frication and by expandable foam; I filled that little square hole with froam when I was finished. I was going to put expandable foam in the tower, but decided against it for the time being. I may go back and do it since it is very unlikely that I will ever remove the copper pipe. I just cut the copper pipe to the proper length so I go get my CO2 bottle in the fridge, but it runs up as far as I could put it in the tower.
As for lining up all of the holes I just drilled the holes in the fridge first and then measured everything and drilled the top and wood at the same time.
The top is black, but it still had the protective plastic on it in the picture, and it looks silver because of the flash.