I've resisted the temptation to install themes or replace any part of CyanogenMod 4.1.99 as installed per the instructions in the original post. I'm using the experimental BFS303 kernel and I haven't noticed the sky falling or portals to a hell dimension or anything. Sweet.
In previous experimental releases of CyanogenMod, I tried my best to reconcile my difficulties with the new Donut-compatible HTC_IME (Touch Input) by reciting to myself the following mantra: "at least it is still better than the Android Keyboard". Well, I've thrown that out the window. I haven't installed HTC_IME and I barely miss it. HTC_IME is so buggy and insolent on Donut that I highly recommend others actually sit down and try out the default Android one for a few days. The only feature I miss is the screen calibration, and it's not even particularly necessary. /shrug
A final comment: it appears the Sapphire 32A instructions provided here are actually more straightforward, simpler and easier than the initial "universal" instructions provided by Cyanogen himself. How odd that something is actually easier on 32A than on 32B. :P
Samsung Galaxy Nexus
) | Android 4.0.1 ITL41F.I9250TDVKKB | Baseband I9250TDVKK6 | Unlocked + Rooted