Problem doing a fresh install of Mountain Lion on replacement blank drive

After a close call in which the internal drive on my late 2009 21.5" iMac needed repairs unexpectedly, I acquired a replacement drive (WD Black 2TB) on which I planned on starting fresh with a clean install of Mountain Lion rather than cloning the existing installation that went through so many upgrades over the past 3+ years.

I now have a perfectly bootable WD Black 2TB drive attached to the USB port of the iMac. I can boot from it, use the Recovery partition if I need to. My contacts and Safari tabs and bookmarks are synced up through icloud. I am even able to install traditional software. Everything appears to work fine except.... I cannot install any application acquired from the Mac App Store.

When I go to the purchased icon of the Mac App Store, all apps show as already installed. I read several articles suggesting holding the option key when clicking on the "Installed" button, unchecking the "automatically install applications bought on other macs" etc. to no avail. A call to Apple Care is requiring futher research. I am now reaching out to the community for advise.

A important hint here is that, for some reason, when I boot from my fresh ML install, that OS sees the internal drive as an extension if itself, and treats all Mac App purchases there as already installed. Using Spotlight to find any of the apps marked as Installed invariably points to the Applications folder of the Internal drive. I have been unable to 'disable' the internal drive or unmount it.

I would rather not swap the drives until I complete a full installation of the OS and applications and data on my new WD Black 2TB drive. But from what I can see, this appears unavoidable. I can't believe I am the first one to run into this situation, hence my call to this community.

Thank you for your assistance.