Best rule of thumb for seat height; when the pedal is straight down 6:00, and your leg knee-locked straight, you want your HEEL (not toe or ball) to graze the pedal. Then when the BALL of your foot is on the pedal you should have pretty-close-to-optimal knee bend at bottom of stroke.

Your first pic shows drive side pedal at more like 4:00, so can't tell anything. Second pic shows NDS pedal at 6:00, and your heel drops significantly lower, so I'd say you need to raise your seat at least an inch, maybe more.

After you get seat height right, then there are lots of variables to play around with in the cockpit department, but I don't know if there are any rock-solid rules of thumb, as it's a matter of personal preference and riding style whether to set for more upright or more bent-over. It's good you have an adjustable stem to experiment with. You've tried different angles, but try also rotating the handlebars forward (down) and backwards (up) in the stem as well, maybe also take the stem cap off, and move the stem/spacers around to try different stem heights. That's three variables (stem height, stem angle, handlebar angle), try riding a decent-length fixed course (around a couple blocks, at least 1/2mi) between changes, only change one thing at a time, try to figure out what feels good for you.