Seat height is correct. Leg's too short. ETT and stem extension are correct. Upper body and arms are too long.
I don't mean to be nasty. My own way of handling a weak core is to avoid exercise and accept the pain of too much weight on my hands, arms, and associated joints. But my seat height is correct - no knee pain riding, but I get knee pain while walking and dancing. (I avoid running, too, whenever possible.) No back or butt pain, either, while on the bike, because the bike's length is about right, and my butt takes only part of my weight.
Moisture, You need to run some more experiments and check out more variables. You closed your mind prematurely, sort of like Donovan did.