So I'm wondering what config files I need to tweak, to help the already installed system use the "new" ahci controller? Previously, it appears to have been using the piix module to access the drive with the root fs on it.
So, you need modprobe.conf to reflect this as well as a new initrd. On a similar system I have from Asus my modprobe.conf looks like this:
alias scsi_hostadapter ata_piix alias scsi_hostadapter1 ahci
I assume the ata_piix is still required for the jmicron ide controller. After editing this, run mkinitrd which will look there and then load the required modules.
HTH, jlc