? Major issues with Win7

OK! Reading more and I had this problem before.....

If I need to reinstall Windows (which I have done before because this has happened to me before). BUT, last time this happened the partitions didn't get messed up. I have 2 HDD (1 w/Vista only 160GB and the other w/2-Win7 1.5TB knocked down to 800GB (to make it faster)). Now when I go to repair the Win7 install disc doesn't recognize the partitions on the 1.5 TB, it had 4 Partitions on it (1 w/1 Win7 installed, 1 w/2nd Win7 installed, 1 w/Backup files and 1 w/Storage (downloads, music, pics, etc..).
I like to reinstall the Win7 over 1 of the existing Win7 to get it to boot up, but since it only sees the 1 OS on the 160GB HDD it wants me to format the 1.5TB HDD. Which I don't want to lose the Storage and backup files.

Now while I am currently on this e-jiffy I can see all my files and OS's are still there(OS like, but with no features like windows explorer, driver access, open files/programs, run programs, etc... but can view files on the drives and a save feature that I guess is just to a cd and not to the HDD.

I guess my question is: If I reinstall windows will I lose everything on the 1.5TB HDD???

I hope this is enough info?
Thanks in advance with any suggestions.

well......................

I guess I will reinstall Window again and hope for the best  
Wish me luck lmao

Well this is kinda of an update:

I reinstalled Windows on the 180gb HDD, which I didn't really want to lose that OS but didn't have a choice. At first the install went the same as any other and it even seem to pick up on the other 2 OSs. BUT, that was short lived and got my hopes all up for nothing. The first time (after updating and installing drivers) it saw my other drive as if it was fine and seemed all good to go. And I even was able to log into the other OS (just the one, the other still had issues) and do things on it like nothing was wrong. But, after being on it evening then shutting it down for the night is where it stops. The next day when I went to get on the old OS it would not boot up and and had the error screen come up saying: "Stop: 0X000000F4 (0X0000000000000003, 0XFFFFFA8005EFCB30, )X............." I wasn't able to write it all down before it restarted the computer. But after that it didn't show the other OS in the boot menu, so I got back on the freshly installed OS and low and behold to my horror it didn't show anything on the other HDD. And that windows gave me problems then. So, again I went to the CD to repair my computer and it showed all of the OS's But would not repair the older ones saying there isn't a OS associated with them. But had to reinstall the fresh OS on the 160gb HDD again.... And now it is all I got  
Even now when I go to Computer Management it says I have to format that drive.

I was hoping I could have access at least until I was able to buy another HDD so I could move everything off of it and start fresh on it or trash it. But I can't do that now it seems unless someone knows what I can do to recover my files on the drive before they actually do get erased for good.