When you said you ran chkdsk from the Command Prompt option was it chkdsk /R
? If not, try it again. You'll have to reboot and it may take hours to complete. Don't stop it. When finished, it will attempt to boot into normal Windows.
Regarding the "rescue disk" you purchased, I suspect it is a Vista Repair Disk. If so, it doesn't offer any further options that the Advanced Boot Options Menu, "Repair My Computer" selection has. If you have been attempting startup repair, system restore, and command prompt, that is what you have been using. There may be an option to recover the computer to factory specifications on that menu. See this post
. I'm not recommending this option yet as all data will be lost
If you strongly suspect an infected MBR, it might be best to post in Bleeping Computer's Virus, Trojan, Spyware, and Malware Removal Logs Forum
. They have experts with special tools to diagnose infections even on nonbooting systems. Just a thought.