It looks fantastic!
Regarding the README:
2.-3. Seems ok to me. These are configuration issues.
1. Maybe we need a way to source that out so that future upgrades don't overwrite that.
4. Shouldn't this be taken care of automatically (after install, after upgrade, after unistall)?
5-6. If this is bad design in Oacs/dotLRN than they have to be changed in general to support future themes. If not than using the theme will be impossible since it will surely break after an upgrade of the site. Maybe you can provide a list of lists/forms that are affected and a solution that works also on the long term.
