They say there's no such thing as a stupid question. Let's give that theory a try shall we?
Is it possible to somehow achieve guiding on an equatorial mount which is misaligned?
I should mention my specific application, today I was doing Comet C/2012 F6 Lemmon while it was immediately beneath the south celestial pole in the Octans.
Naturally right underneath the pole is not a position I can put my mount into. Not everything is as upside down in Australia as the northern hemispherians like to believe and my mount was certainly not attached to the ceiling.
Anyway I eventually got my comet photos unguided without tracking and by limiting my exposure times to 5 seconds.

I know. What's worse is how I found the damn comet. I pointed straight above it using the computer, measured how many degrees down the scope needs to go and adjusted the altitude screw on my mount.
Anyway here we are not only are we not aligned to the south celestial pole but sidereal tracking would actually go backwards given how I've just set up my scope.

And naturally PHD had a meltdown.
So with that in mind is there anyway software, or technique or otherwise to track something below the south celestial pole other than using some magic floating plinth for the equatorial mount?
Cheers.