I believe you just put the cam back in the way it came out. You are correct in taking one out at a time, this will hold the cam chain in place without worrying about it dropping into the head. There should be numbers on the sprocket side of the cam to assist in lining it up right. As for wet sanding the shims, I was told just to go to a local bike shop and they will either sell you the right size, or swap yours out with the size you need for no xtra charge. I speak from the advice given to me by fellow SMJ'ers and TT'ers, as well as online tutorials found on TT and ADVrider.com

My exhaust valves currently are at .18......I need to pull the cam and swap the shims too

I think you aim for the middle for the valve clearance (.15 for the intake, and .25 for the exhaust)