Brian this is a great post but may overreach for some to understand though I do agree with you with one added observation/insert.
Most know I am a big believer in weight training and though you mentioned both quads and hams the one area that did not get mentioned was the strongest muscle in the body, the glutes. Depending on what type of deadlifts you are doing (Romanian or stifflegged) the focus will be slightly different but while weight training I believe there should be an emphasis on glute training as well (squats, deadlifts, leg press).
I do think you are on point to realize something and put it into practice, you have gone from engaging one muscle group (quads), are starting to incorporate two (quads, hamstrings) and once you bring in the big daddy of the lower half (glutes) you will see another big jump.
Next time you cool down on the spin bike do a couple of minutes on each leg with only one foot on the pedal, on a spin bike you will really feel the activation of the glute as a spin bike doesn't allow for dead spots in the pedal stroke.