What I would do is do this same process to each HDD that has a Windows 7 installation, separately, do one with it only connected then disconnect that one and do the second, that way they will boot independently of each other using the BIOS one-time boot menu instead of the Windows boot manager; that way they won't be 'tied' to each-other.
"Also do I need to remove the install dvd that is my external dvd drive?"
You lost me with this one, do you mean to remove the installer DVD from the DVD drive; if you do that how will you boot to diskpart?