Won't Load After Using Compaq System Recovery

Recently, my computer had been running rather different than normal, and I felt that something disastrous was going to happen soon, but I took the stupid route of simply doing nothing and excusing my hunch as nothing more than the computer being old. Pompeii 2 decided to take place on my computer. My "hunch" was very correct, as yesterday, multiple trojan downloaders showed their ugly faces, and placed nearly every virus known to man on my desktop. I then proceeded to but windows in safe mode, unplug the ethernet cable, and run Trojan Remover with the latest updates. Well Trojan Remover did quite a little number on my comp, disabled svchost's from running, and made it impossible for me to connect to the internet. After rebooting again, Windows was unable to boot and a box popped up stating that lsass.exe could not be found. I then booted into Compaq System Recovery and performed a "Safe" recovery that doesn't delete data but restores everything else.