We still don't know what happened to your windows. Changing a battery should not have caused this. Brainstorming, I am thinking some BIOS settings may have changed, confusing the software. If it triggered WGA, a full reinstall may be needed. Or something else may have got disturbed while you were working inside the box. Double-check every connector and setting.
Booting from CD: when you enter "linux root=/dev/hdb1 ro" on start (assuming hdb1 is where you installed VL), it boots into your Linux install as if you booted from the hard drive. You then have full access to all the tools like vasm etc. You may be able to repair the problem from within VL, maybe not. If windows system files are damaged, you will need to extract them from the windows CD. The windows recovery console contains scripts that do this, but it is very limited.
Of course, I highly recommend you back up any important files first. There is always risk of data loss. You can boot up VL and use it to read/copy the files, or use a LiveCD version that doesn't write to the hard drive at all.