This has been working fine and I've these additional discoveries to share:

• Windows sometimes randomly chooses to recognise file ownership or something and won't let the script update the config files. Restore the originals and restart the command prompt and it works again.
• cpan sometimes leaves it's lockfile locked and can't reset it. Delete it and try again and it's fine.
• Any CPAN configurations in your C:\Documents and Settings\Username\Local Settings\Application Data\.cpan will override the settings elsewhere, including your stick. Delete that too...
• Using o conf in CPAN will often make the config file unreadable/unwritable to the script. Delete it, restore backup...
• Using CPAN's autoconfig can be unpredictable. If it shows up the script failed. Fix whatever caused that first. ...you might also consider restoring those backups too...
• Flattening the include libraries doesn't help with the compiling. Mostly it seems to be Makefile or Makefile.PL that have shell components that fail... or more likely dependencies I don't have. At least you don't have to restore the backed up config files.

This tells me I need to make a roll-back script that restores those config.pm.orig files I carefully backed up and removes the cpan lock file, and I need to carefully put together my compile libraries.