Great work and effort!
I had the same issues, uploaded the latest branch and the dropdowns seems to be working now!!
In the frontpage the blocks section is duplicated. I have a blocks section on the right (and that's ok), but the same blocks section appears in the bottom...
this is the relevant source code:
...
<aside id="block-region-side-post" class="col-3 d-none d-md-block block-region yui3-dd-drop" data-blockregion="side-post" data-droptarget="1">
...
<aside id="block-region-side-post" class="col-3 d-none d-md-block d-print-none block-region" data-blockregion="side-post" data-droptarget="1">
...
so you see there are different classes applied to each section