It's working great now! Better than I had it yesterday, and I've reduced the whole XSLT portion down to 46 lines of XSL code separated into 2 files (one to produce the WebObjects .WOD file, the other to produce the modified WebObjects .HTML file).
I removed my hand-coded XML-to-HTML cloner, since it was waaay to possible that I'd miss some HTML entity or attribute and have themed pages munged without explanation. The new method takes 6 lines to exactly clone any element that I don't explicitly deal with. Very cool. And that removed 1 extra XSL file, and an additional 98+ lines of code.
XSLT really CAN do anything... Now, why on earth isn't it included in WebObjects as a core library?