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Don't be afraid to change things up on the ride. The best thing I ever did was to get a seat pin that is really easy to adjust so I can move the saddle back and forward or adjust the tilt independently. What length stem are you running? I bought an adjustable angle stem to play with until I figured it the right handlebar height and reach. Looks ugly as hell, but allowed me to dial in the position in a few rides. Now I've swapped it out for Deda that matches the best position I found.
And doing longer rides certainly amplifies any niggles, first thing I did after a 200km a couple of months ago was whack some more spacers under the stem.