Ahah!
Well let me make sure we're clear on the difference between "rebuilding an iso" and "remastering an iso". The first process can be done in windows or linux and will allow for only minimal changes because the vast majority of overclockix is contained inside a cloop-compressed file called KNOPPIX. When rebuilding an iso, all you can edit is stuff outside of the cloop. That would be client.cfg, the boot codes used by default, and the bootup splashscreen.
To change what stuff runs as the system is starting via init... for instance vnc, for presetting a vnc password so you don't have to set it while the system is booting, and for let's say changing the GUI vnc uses (set to kde by default currently), that would take remastering the iso.
Remastering takes about an hour or so. You have to have a linux partition large enough to hold the uncompressed contents of the CD. You'd boot from the CD, extract the contents, alter the things that need altering, such as default configurations found in /etc/skel, or init scripts. Then you'd have to make a brand new cloop which takes a lot of ram and swap (1GB+) and anywhere from 25 minutes to an hour of processing, and from that build a new iso, which takes a minute or two. There are VERY good guides to remastering at
www.knoppix.net/docs
In particular setting vnc to run at startup would take-
Soft-linking one of the handy vncserver scripts already included in the distro into the default runlevel's run control directory. Editing /etc/skel/.vnc/xstartup if you wanted vnc to run something besides KDE on the remote system. And writing your own script to take a vnc password file and place it where it needs to go so that the password is preset when vnc starts, rather than have it ask you to set one while its booting up. I'd have to play a bit to figure it out. I used to have vnc run by default and just have the user set the password during bootup.
So how much effort is this worth to you?
You can always bootup and then from your windows box use putty to ssh into the overclockix box, startvnc and set the password. You could even edit /home/knoppix/.vnc/xstartup
to change to fluxbox or icewm if you don't want vnc using KDE.
FYI there are scripts vnc800, vnc1024, and vnc1280 which start vnc servers at various resolutions. These are available as if they were system commands.