I finally figured out a way to get the Carbon port of Emacs to use another font than Monaco 12 for windows (or frames in Emacs parlance) after the first window.
The obvious custom-set-faces only affects the first window, but the following works:
(cond ((eq window-system 'mac)
; needed for subsequent windows because custom-set-faces somehow
; doesn't apply and we reset to Monaco 12 otherwise
(setq default-frame-alist '((font . "-*-Monaco-*-100-*")))
I had a few hours to work on ICeCoffEE over the weekend: it went well, and I've implemented some preliminary Carbon support. My research is sucking up considerably more than the usual amount of time this week, so it'll probably be Saturday until I get a chance to finish.