This is amazing work! Played the first four levels on Vice, and I'm about to give it a go on real hardware using my KungFuFlash.
One question—was it a stylistic choice to only use the noise channel, or was it motivated by economy? I only ask because the iconic Wolfenstein item pickup noise is just a short series of bass notes that could be easily replicated by the SID, and it could go a long way to evoke the original. Maybe in a future point release?
Having read the other comments, I would also echo the request for a mouselook option, but only having 50 non-contiguous bytes, sheesh! Doesn't leave much breathin' room. And that may also answer my question as to why you didn't include the item pickup noise.
But holy cow, it's a really impressive piece of work you've turned in here.