I've taken a copy of your site so that I can have a look at it without worrying about breaking anything on a live site.
You have quite a lot going on in your site in terms of plugins etc. and the first thing I have tried to do is to isolate how Toolset is involved.
It looks like a problem with your child-theme.
I disabled all plugins except WooCommerce (including the Toolset plugins) and viewed a product on the front-end as rendered by your theme. The main content is full-width with no padding so that the sidebar is pushed to the bottom, as you described.
That is with Toolset disabled and with the product rendered by WooCommerce using your theme.
So I switched theme to the parent Genesis theme and that fixed the problem. The product layout looked normal, with the sidebar in the correct place.
I'm not very familiar with the Dynamik-Gen theme, but that's where you need to focus.
If you get the normal WooCommerce product display to look okay but then your custom Toolset product template doesn't, let me know and I'll take another look.
I've dealt with the custom fields issue in the original thread.
Regarding the layout of the product category archive, is this a problem with the child theme again? If you switch to the parent theme, does it display sensibly with the sidebar in the correct position?
