Got it working now
Well, it was a lot of trial and error in the end. First, installing it was a pain, cause I had no medium to boot from (USB sticks not working, USB-CDROM/USB-FDD would). I ended up using unetbootin with the harddrive install option on the win2k partition.
Then, i compiled an additional kernel module for the graphics unit (don't actually know if that was necessary in the end, have to test it..). And in the end a lot of trying different xorg.confs, Modeline settings and grub2 parameters.
Regarding emulation, yes, that is the next step now. I am not really sure what the best option would be. After talking to the QEMU guys, they don't have support for ISA passthrough, although that shouldn't be to hard to implement rudimentary if there are no interrupts involved (I don't think there are any for the interesting boards, win2k drivers only show I/O and mem (except for the MacSpeech board?)). Getting DOS running in QEMU is easy though.
Dosemu (abandoned, dosemu2 is active) on the other hand could potentially have support for it, but it is much harder to get DOS running there...