To correct windows problems you can probably do a "upgrate" which would keep your programs and your data and only rewrite windows files. I'm about to test that theory out on my wifes computer, as she also has windows problems.
On installations of windows for larger HDDs.
1) Always partition the HDD so that the first partition is only 200 gigs +/- 100 gigs. This is for just the OS + Programs and will be the "C" drive. The remainder of the drive will be your "D" drive and is for all YOUR generated data.
2) Eilieminates the problem you have with "wiping the OS" and re-installing.
3) Once you have windows installed on New HDD(remember DISCONNECT first HDD before installing windows on 2nd drive), install all Drivers, programs and test.
.. Use windows Back up to create an Image file of your "C" drive and System partition: You will be able to re-store your system to exactly like it was when image was mad - NO MORE: re-install windows, Wait for Windows updates to be installed,, NO reinstall drivers, NO reload programs!!!
On win 7 and Vista you can also do a custom install onto the partition where windows is stored using an OEM, Upgrade, or retail disk as long as you have enough free space to install windows. The new copy of windows will move the old one into a folder called windows.old which will hold a copy of the users, program files, program files(x86), windows folders from the previous installation. Just remember this requires a good amount of free space to do which you can recover afterwards by deleting the old copy of windows after recovering your files.