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I did get a fit before purchase and then when I had it to make sure it was sized correctly and all seemed correct and proper. I've messed with shorter and longer stems, seat position and bar position to see if I could get some relief.
In the end I think it might be that I just bought a bike that is too aggressive for me to ride comfortably? That and my balls don't like being knocked about on three hour rides.....
To be fair, the bike does sound a little on the large side base on your description.