You are braver than I am! Last week I was about to convert my regular WP install into a multisite, and then I realized what a pain it’d be to rework all the links and permalinks. I ended up keeping the single WP site for my main blog and adding a separate multisite installation into a subdirectory. That’s two blogs to administrate, but the mod_rewrite work was too daunting for me to tackle in the time I had set aside for it.
BTW—I love the new theme! Very clean and readable!