Congratulations on your purchase and hope you have many happy miles on it. I had almost exactly the same problems when first riding my 2010.I put on 2 inch Genmar risers and the seat mods and cushion below which eliminated the shoulder pain, leg cramps and squashed boys.
HANDLE BAR Risers - Search the forum for Phil's wedges and see whether they may not be part of the answer particularly for wrist problems. Fortunately I didn't have this problem but a lot of members did. While Phil no longer makes them they are available at Murph's (
http://www.murphskits.com) and may be used in conjunction with risers. I did see a site where the wedge angle was incorporated into the riser but cannot find it now.
LOOKING AFTER THE BOYS. - I thought that I was the only one who had this problem , sympathies to a fellow sufferer. Here is what I did to make it a bit better.
1. Boxers did not provide adequate support so I tried out various brand and designs until I found one that helped. It almost like a pair of Jockey skants but lifts them out of the way.
2. I had the front of my saddle flattened and had a piece of very soft foam put in the middle running length ways. This foam did not really help as the vinyl prevents it sinking in. I then made a cushion after seeing the latest Airhawk design using 38 mm soft memory foam with a cut out . This I put into a cover made by my wife with some straps . See pics below.(Sorry , converting to PDF's which cut the size affects the orientation- haven't worked how to fix it) As the material on the cover is a bit loose it allows a bit of room and creates a welcome space.
You may find as well that the cushion which lifts you up a bit will also help with the leg cramps.
