I went ahead and did as you suggested — well sort of — I replaced only the files that had been modified with fresh copies from the initial install. When I changed the height of the header again, sure enough the color switcher ended up where I didn’t want it.
So, I took a look around in the template_css.css file and found:
.ja-color-theme {
position: absolute;
top: 228px;
left: 10px;
A minor adjustment to the top position in this area did the trick, putting the color switcher information right back up where it is supposed to be! 🙂
I initially found the information on reducing the size of the header in this forum, but the resulting changes that (might be) necessary in the placement of the color switcher information were omitted. I hope this helps!