Don't worry about centering the master cylinder with the hole in the firewall. The rod alignment is what matters, like you said. My master is completely off center of the OEM firewall hole (but perfect rod alignment). It's definitely tricky to do, especially alone with no help, which was my case. I spent at least an hour checking over and over again, climbing in and out of the car, to make sure the position was right before drilling the mounting holes.
