Windows 7: Hard Drive complications

I upgraded to windows 7 (not a clean install) and after doing so, I'm really happy with Windows 7. But all the programs/games I have on my separate, larger, hardrive (where my OS isn't installed on) were more or less boxed in, and I had to go into each file and create a shortcut for my games and toss it on my desktop. Some other programs, such as my anti virus, I was not able to do this with. I'd rather not have to go and download some of my programs again to fix this, is there some way to make it right? Would a clean install correct this? Also it makes it alot harder to re-download my programs because my 2nd hardrives programs don't even show up on my add/remove programs list.

I think your other thread sums things up a bit. Getting rid of Vista for 7

Once you upgraded to a different version of Windows you started off with an entirely new system registry. For seeing all the previously installed programs running again as well as shortcuts they would need to see a fresh reinstallation of each for those that needed more then a simple shortcut from the main executable.

None of those would be seen in the Programs+Features until installed in 7 to start with. At this time they are simply folders left idle on the second drive. A clean install of 7 at this point will also require a full install of every program you formerly had running on Vista.

One of the big drawbacks when custom installing programs onto separate partitions and drives is seen when upgrading. Was that the 32bit or 64bit Vista previously on?

Yes, my vista was 32bit, I wanted to try 64bit when I installed Windows 7.

Edit: I'm sure I'll end up looking the following question up, but would more then appreciate you answering it Hawk. When windows 7 is released, will I have to reinstall Windows 7 after I buy it, despite owning and operating the beta? I'm very much assuming the answer is "Yes, you will need to buy and reinstall your Windows 7 when it is released".

I thought so! That's why MS provided some answers already to quesions like that one. Windows 7 Help & How-to

"Can you upgrade from the 32bit Windows to the 64bit?"=querstion You won't like the....
MS answer=
Can I upgrade from a 32-bit version of Windows to a 64-bit version of Windows?
No. If you are currently running a 32-bit version of Windows, you can only perform an upgrade to another 32-bit version of Windows. Similarly, if you are running a 64-bit version of Windows, you can only perform an upgrade to another 64-bit version of Windows.
If you want to move from a 32-bit version of Windows to a 64-bit version of Windows, you'll need to back up your files and then perform a custom installation of the 64-bit version of Windows. For more information, see Installing and reinstalling Windows**."

For the second question = "Can I upgrade from the RC to the final version of Windows 7?"
MS answer = "When you install the final version of Windows 7, you'll need to do a clean installation. So plan on backing up your data then reinstalling your applications and restoring your data." http://www.microsoft.com/windows/windows-7/faq.aspx