2) It'd be awesome if cgminer would record the current clocks on startup, and restore them on exit if the auto tuning changed them at all.
Are you having trouble in that department, or did you just miss this?
STARTUP / SHUTDOWN:
When cgminer starts up, it tries to read off the current profile information
for clock and fan speeds and stores these values. When quitting cgminer, it
will then try to restore the original values. Changing settings outside of
cgminer while it's running may be reset to the startup cgminer values when
cgminer shuts down because of this.