If the side with the batt wires is heating up, the source of the extra heat is likely the capacitors. Even the guys at S&T will recommend that you add extra capacitors to the Quark when running it in a large scale truck. When I called about my setup, running 5S with an 8XL, Frank said that extra caps are very much recommended and the more the merrier. Since I've added the extra caps to my MM and Quark speed controllers, they do run significantly cooler. The MM is also handling gearing that it wouldn't handle before without cogging.

Here is a pic of the first cap bank that I made, wired to a MM.