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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.
Yeah - it's funny, doing a long ride is almost a 'shortcut' to realising what's wrong with your fit if it always feels like 'something' is off but you can't place it on a 'normal' ride.