I've read that capital ships should dismount their weapons in order to avoid compatibility problems with the new mod.
Done and done.
What about Guard IDs? Since Guard IDs are being eliminated (exceptions being the BH Core and whatever the new Nomad faction calls itself), should the Guard IDs be sold now and replaced with regular faction IDs?
You do not need to unmount anything. Unmounting guns might make it easier when the version switches, but more than likely it will not be necessary. You should still be able to unmount everything when the version swaps. It will only boot you from the server if you try to undock with them mounted on a spot they can no longer be mounted on.