You are good. Don't worry about the port0 thing. The way you did the installation, it is irrelevant.
The reason why it is recommended to have the designated OS disk on port0 is because the Win7 installer has this habit to install the bootmgr (and often the 100MB system reserved partition) on the disk with the lowest port number.
But since you installed with only the SSD connected, this problem did not occur. And the reason why you did not get another 100MB active system partition during the reinstalltion on the SSD was because you already had a primary partition on the SSD into which you installed.