Daniel,
I saw your modifications done for HP 200LX, so don't tell me that Zaurus would be too difficult for you
But of course you're right about compilation part, having a working build environment is a must, since many hardware changes require the appropriate changes in the software. Speaking of which, I'd suggest to go with either pdaXrom or OZ/OE, since both of them have open source build environments. Sure it's possible to re-compile the kernel and write applications for Sharp Qtopia-based distributions too, but you may find yourself handicapped at some point due to lack of open source code.
Also, the Zaurus is quite a survivor device, IMHO. During my experiments, I used to connect wrong signal lines, wrong GPIO pins and it's still not damaged. I doubt that it's my luck, so probably it's not that easy to be killed.
-albertr