The two holes are tapped into the top of the Z column, where the Sieg factory puts the plastic plate / cover (the cover gets removed for the conversion- I popped mine off running the head off the mill to clean it when I got it). It's to provide additional stability for the Z motor mount. My Z is solid AND fast!!!
I've got a bit over 8" of travel in Z with this retrofit. I drilled and tapped it by hand, with a cheap tap, even.
I have dual-shaft motors, and may mount some handwheels on it, but once I've got it finished up, I probably won't use it manually again.
It was a pretty harsh sound, like a rattling... You mention on your site to listen close to the audio... (fignoggle_badSounds.wmv)