I'm on the same path as you. I have lowered my saddle until I have a decent knee bend with a flat foot. That alone has saved my ass and solved a lot of uncomfortable saddle issues.
Then, working on the fore/aft. I have also started around knee cap/end of crank. Too much weight on hands though so I moved it back, under about 1cm. I feel balanced but my bars feel a bit too far out. Causing some elbow pain. If I go too far back I get perineum/soft tissue issues. Handling is also affected by this. Too far back and front end is not planted on turns.
Bar drop has also changed a lot. I am currently with a 1cm drop. Once I get a FSA Wing Pro Compact, that will change a bit I think.
Also, I am considering getting the Speedplay extension plate so that I can put the ball of my foot about 8mm forward of pedal spindle. This will allow me to lower saddle and lessen the bar weight without pulling the saddle back too far.
Lastly, I have learned that sitting properly on the saddle makes a huge difference. Sit on your sit bones, don't turtle neck and bend at the hips not the lower back. Ride with a rounded back and shoulders, slight bend in elbows. Steve Hogg's articles have been very helpful. Pelvic stability on the saddle is paramount.
Incidentally, my two "pro" (static) fits from Serotta fitters have left me less than satisfied and learning what makes me feel better has been more helpful. Being willing to try different stems, saddle heights, fore/aft have been a learning experience.
Hopefully, I will have my "perfect" fit figured out very soon. I can say that I have not experienced any back pain, neck/shoulder pain or knee pain.