If you have both an electrical engineer and a machine shop at your disposal it would seem almost criminal to not utilize them...most of the modding addicts here would trade a kidney for those personal resources. If I were in your shoes, I'd use the DNA20 as a reference and issue a challenge to your EE buddy to come up with something better, or at least something
yours.
As for charging, a phone charger would take a very long time to charge parallel 18***. Of course if you already use the same batteries in other applications, having a spare set or 3 will be necessary anyway, thus eliminating the need for USB charging. The Nitecore I4 charger is great for any kind of battery given it's charging speed and ability to juice up 4 at a time.
Also keep in mind that two 18*** take up a good deal of space. If you're ok with an APV the same size as say, a personal defense flashlight, then never mind. Also check out
side-by-side type mods for innovative examples of how to skirt the issue.