New
#11
Assuming that the install disk for windows 7 has not been compromised - downloaded and burned to disk from an infected system - then there is no way that the new seven install disk can be infected - the fact that you boot from a clean medium, either the install disk or partitioner disk, ensures that the memory is clean.
once the install is completed the system should be clean and thus can be used with suitable AV software to clean the external drive.
The only infection that could possibly survive this procedure would be the extremely unlikely one in the system BIOS - if this is a concern then you would need to re-flash the BIOS from a clean external source disk, before any other operations.