OK, so for steam, whut you do is this:
once the OS is installed, drivers, etc, go into the STEAM folder, and rightclick the STEAM .exe and select "run as administrator".
This will make STEAM reset the installation routine for all apps, allowing a fresh install of the games when you first start, without and data loss, and no downloads(minor downloads for file verification). Each time you start an app in STEAM the first time, the install will rn, and you can be sure that your STEAM apps run properly.
Basically everything else is FUBAR'd.
What you can do, if you are using the same drives, etc, you can backup your registry, and then replace it, however, if you are re0installing because of OS issues, this might be the last thing you really want to do.
So, I recommend jsut re-installing the other apps outside of STEAM.
I do do this very often, and very rarely do I have any issues with activation, or such stuff. All my software is legit, so if something doesn't work, usually a quick phonecall to the app maker, and it gets sorted.
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All that said, all teh data on the secondary drive will still be there, so your music and pictures should be safe. Jsut make sure you do not install windows with that drive plugged in...leave it unplugged from mobo until you finish windows install.