You want a booted install with only target HD plugged into Sata1 port, so that Windows 7 will see itself as C when booted - which it won't if installed from another OS.
Follow these steps to get a perfect
Clean Reinstall - Factory OEM Windows 7
After install plug back in the other HD to access it's data from within Explorer, making sure to keep the new HD set first to boot in BIOS setup. If you need to boot the old HD, at bootup tap the Acer F12 one time BIOS Boot Menu key then select the other HD by make/model.