Hey there KZK RECORDS
I'm still a bit confused as to why it's not working this fix for you.
Every Apple machine comes with a pre-installed OS, you can't install an earlier version than the one it came with.
So if your MacPro came with Lion, then you can't go lower than OS 10.7.x, if you try to install your Snow Leopard 10.6.3 directly into the hard drive, you might as well look at the wall and wait forever since the MacPro will get stuck on a Loop Load.
Now lets go to your MacBook Pro, which from what i have read, it's currently in Leopard OS 10.5.x, first suggestion would be, can you install SL 10.6.3 onto your MacBook Pro? The only reason NOT to upgrade your MacBook Pro to Snow Leopard would be that your laptop has in fact a PowerPC processor, but if this is not the case please do upgrade your MacBook Pro's OS.
I strongly recommend it!
If you can install SL onto your laptop then you should be good to go and install PTHD9. Once installed, again Hook up your Laptop via Firewire to your MacPro, start your laptop first as Target disk mode ("T" key) and then start your MacPro with the "Alt / Option" key in order to select the Boot drive you want the MacPro to start with (Choose your laptop from the options).
If everything works up to here, then proceed with the Firmware update and you should be good to go with your PT HD Native system.
Last but not least, you also have an External Hard Drive, so if you were to install a Bootable OS from an external Firewire Hard Drive, you have to make sure that the Hard Drive has 1 Partition and it has to have the "GUID Partition Scheme" Format for it to work as a bootable external hard drive.
Please follow Apple's instructions on how to format a bootable external drive posted here:
http://support.apple.com/kb/TS1600?viewlocale=en_US
Once you've formated your external HDD, proceed to install the SL OS10.6.3 and the PT HD. and finally rinse and repeat the process of starting your MacPro with the OS from the HDD for the Firmware update.
Hope this works for you.
ps. I'm assuming that your external HDD is Firewire, according to Apple's documentation, USB drives should also work, but for the sake of it i'd rather do the procedure with Firewire.