It was raising the saddle and putting a longer stem on that made the bike more comfortable. So to make it even MORE more comfortable, I should lower the saddle and put the shorter stem back on. Got it.
I was unclear. I apologize
You may have pulled more seatpost out of the seat tube, but by moving your seat forward, you effectively lowered the seat. Your toes point down, which
may mean the seat is too high..In moving the seat forward, you also decreased the distance between seat and handlebars, effectively shortening your stem.
Your arms look fully extended. If I draw imaginary lines and triangles, I don't see much margin for bending your elbows, even with raising the 'bars. If you ride with your elbows straight, you make yourself vulnerable to hand, wrist, elbow, and/or shoulder pain. Moving the bars up further shortened the distance between your butt and your 'bars. You don't include a photo, so we can't see how much you bend your elbows. My triangles may be off more than I think they are.
Looking at your photo, I have a hard time seeing how the bars can obstruct your view of the front hub. A straight line from your eyes to the hub looks unobstructed by the 'bars.
If seat-pedal and seat-'bars spacing is to your liking, that is what counts - but with toes pointing down and your arms straight, the spacing doesn't look all that great for you.
I think you may have pain because of your position if you take 2-3 hour or longer rides. If you do, it's likely to be because your seat is too high and/or your 'bars are too far forward. If you experience pain on rides longer than an hour, I'd suggest changing your seat height. first, because it's a lot easier than changing a quill stem. If pain persists, replace the stem with something shorter.