A spyware installed some programs that were running in the background so I booted in safe mode and it froze on the xp user list . so i reset the system and it said something like missing OS/files not found. after tinkering with it a little later, I just put in a second hard drive hoping to atleast recover some data. the second hdd had win98 so i installed xp on it. while it was going through the installation it started to check the disks thats when it started to repair the files on the old hdd saying something like bad index. after the install i was able to back up some info from the old hdd but then again after removing the new hdd and a reboot it said it missing OS. so after rebooting from the new hdd again it didnt recognise the old partition on the hdd and said it needs formatting. the bios and xp recognise the hdd but not the partition. i dont want to delete the partition or reformat it as i dont want to lose the data. any ideas on recovering the files?? thanks

Correct me if I’m wrong, but here is the scenario as I understood it:
Windows XP on the old drive is corrupted and not allowing you to boot it, you installed a new drive with Windows 98 on it and upgraded it to Windows XP, you were able to see the files that you needed to recover on the old drive and were able to copy them to the new drive, you disconnected the new drive and tried to boot from the old one which did not work, and finally, you connected the new drive again and now the partition on it is not recognized.
You can go two ways about this situation:
1- Repeat what you did by installing Windows XP on the new drive again, and then get whatever data that you need from the old drive, but this time make sure you burn them to a CD using Nero or any other burning software before doing anything else.
2- Install Windows XP on the old drive, install data recovery software on it, and then run it to recover the files from the new drive; you can find some data recovery programs here:
http://www.snapfiles.com/Freeware/system/fwdatarecovery.html

You've got it right. At the very beginning I had also installed the drive in other systems as a second hard drive and they all recognized the drive but not the files. As I was upgrading win98 to winxp on the older system it checked all disks for errors and thats when it started to make corrections to the file index on the drive. I was then able to see the files and backed up some info except the ones that were password protected under a username. After a reboot the problem appeared again and it was back to square 1.
Step 1 wont work as installing xp on the old hard drive with the inaccessible files requires the drive to be formatted and partitioned like as if its a brand new disk. Looks like the index table on the partition is corrupted. If I was able to recover some files from it before then theres gotta be a way to recover more data from that drive as the files are still there and windows probably wont recognise it due to a damaged index.
I'll try step 2 and see if it helps.

Tried step 2 was able to recover some files but not all of them. The rest I guess are gone. thanks.

"I was then able to see the files and backed up some info except the ones that were password protected under a username."

How to take ownership of a file or folder in Windows XP
http://support.microsoft.com/default.aspx?...kb;en-us;308421

I’d say don’t just give up on them; if you were able to recover some of them, then there is a possibility that you could recover all of them. There is more than one data recovery program in the link that I posted above; so try as many as you can.