Since then, I wanted to add a very elegant slide gallery, SuperSlider-Show (http://wordpress.org/extend/plugins/superslider-show/), which as it happens, also makes use of mootools. At first, the gallery refused to work no matter how I played with the options. After hours of cut and try, I noticed that mootools was being loaded by both my sliding door menu and SuperSlide-Show, so I removed the statement from the sliding door code, loaded the gallery page, and viola! Everything worked perfectly - the menu and the gallery. BUT, on every other page, the sliding door menu refused to slide. After more hours and gallons of coffee, I found a solution:
The SuperSlider-Show WP plugin has a configuration option to disable its loading mootools in case someone else has done so already - that got my sliding door menus working on all pages, but now the SuperSlider-Show gallery was broken again! What I did was go back to the Atahualpa Theme Options->Add HTML/CSS Inserts->HTML Inserts: Header, and replaced my old call to load mootools:
I guess the lessons learned are: jquery has to load prior to mootools; two copies of mootools don't play well together; and some plugins using mootools need the complete set of libraries, not just the core.
Now, if we can just get the plugin authors to check for previously loaded tool libraries, see if they are usable for their code, and conditionally avoid multiple copies (and warn us if the previously loaded versions are insufficient), life would be much easier!
[If I ever get serious about writing a new plugin myself someday, those words may come back and bite me!]