Is the HD IDE or SATA? If its SATA try setting up the controller as AHCI in the BIOS. If its IDE you may need some other kext to get it supported, AppleNForceATA doesnt support some newer nForce IDE controllers.
It should not matter if the drive is not master as long as there is no controller with a slave disk and an empty master port. It should not matter at all if the drive is SATA in AHCI mode, but its always safer to connect the drives following port order.
Bootloader should not be a problem if your system already starts up booting (Darwin prompt, press F8, etc.), means its already installed and working.
About install options, you should ideally choose only one for each piece of hardware (i.e. one option for SATA, one for Video, one for audio), as installing several kexts for the same purpose can cause troubles (specially video injectors).