I don't know if you do or don't. It just seems you are saying stuff works for you that goes opposite of what I'd expect. The "cracking" your knees to me implies you are nearing or in the point of hyper extension of that joint. Which is something you would lower the seat to avoid. But you seem to go in the opposite direction and need to experience it to keep from having pain if I read you correctly.
Even climbing hills your gearing on the bike should let you pedal somewhat easily up all but the hardest of your normal routes. So even if you are not using muscle to pedal while straight and level, then using an obscene amount of muscle to get you up any and every hill will still leave you, me and many others with knee issues. If your bike isn't appropriately geared for your fitness level and the terrain you ride, then something needs to change.