Hi,
Interesting problem, I am thinking of doing fresh install of Windows 7.
You say your second hard drive is now in 3 partitions, but it wasn't before? How many partitions did you have on the 2nd hard drive before install of windows to first hard drive?
I have noticed whilst working on other computers running Windows 7 and higher that there seems to be a recovery partition, used for rescuing dying installs of windows.
The best and most safe way (the way I would do it) is to download a bios based program like ultimate boot cd, then run 1 of the hard drive reader programs (partition manager) and this will tell you what files still exist and on what partition. Then you can boot back up into windows and copy all the files you want to keep to the primary hard drive, then completely format the second hard drive in to 1 partition then you can put everything back on the 2nd hard drive as you want.
Steve