You're being a bit paranoid, and are extrapolating incorrectly

. Your current Xbox and hard drive boot quite happily, so even if your BIOS has issues with the clock not being set, the dash files you need to overcome those issues and set the clock are on your current hard drive. If something goes wrong while you are upgrading the drive you can just re-install the current hard drive and you are back where you started.
To do the change, power up your Xbox for an hour or two so the clock capacitor will charge, before you make the swap. That way even if your BIOS has issues the clock will still be set, so you won't get Error 16 and you should have easily enough time to boot AID and reformat the new disk.
Finally, all recent copies of AID have loads of BIOSes that bypass clock check, and support LBA48 (and hence large hard drives) and on-disk partition tables. The Xecuter 2.6 is 2x512kb banks, so X2.5035 will fit and is probably the best choice. This means that if the current BIOS doesn't recognise the full size of the hard drive you can use AID to flash a newer BIOS onto the second bank of the X2.6, again leaving you the current BIOS bank intact in case anything goes wrong.