I don't have time to analyze things in-depth, but I did notice that you just nested the "autoKill" incorrectly:
//BAD:
.to(window, 1, {scrollTo:".footer", autoKill:false, ease: Power0.easeNone})
//GOOD:
.to(window, 1, {scrollTo:{y:".footer", autoKill:false}, ease: Power0.easeNone})
It's fine to pass a string like that directly to scrollTo, but if you're defining more values that are scrollTo-specific (in this case "autoKill"), you need to use the object syntax. I suspect this is what was causing the dragging of the scrollbar to kill functionality (doing so killed the tween).