Clyde1820

Some observations and guesses ...

I agree that general alterations of the saddle height, stem and bars are probably a good place to begin.

Saddle height -- looks like it's high; knees too darned straight. I agree with the others, on this.

Stem/bars -- looks too low, from the photos; could go to a Ritchey (or similar) adjustable stem that's not too long (ie, their 90mm version), along with some moderate riser bars of the "Northroad" sort. Perhaps a Soma Clarence, on the mild-rise end of the spectrum. Perhaps something like a Jones H-Bar Bend or H-Bar Loop. Too low, for me, puts a kink in the shoulders and neck. Tall enough for the basic riding position I prefer, and I'm good; those aches disappear.

In my experience, fiddling with the "right" combination of saddle position, stem and bars yields the most benefits, assuming that the basic fit and geometry are in the ballpark. But it's very subjective, as everyone has a slightly different preferred riding position, a different level of fitness and flexibility, etc etc.

By the way, I've never stuck with the as-delivered saddle, stem or bars. Never. A bike's geometry has gotten me close, but the fine-tuning required has always resulted in fiddling with those three things in order to get the feel right. Can often be relatively minor adjustments in angle, rise, sweep, etc, to nail it.