You maybe in the poo,

sorry to say donut, What I would do is invest in a larger second HDD, they are very cheap nowdays, then purchase Ghost, I got an old 2003 version on ebay for $12 and works a treat, backs up your whole drive C in one hit, if a bad virus hits or I have done something to destroy the register etc I just re-ghost to a former image (I ghost around once a month), ghost runs then reboots to the former image, done!! It certainly looks like a rebuild at this point, I would backup all your files then do a rebuild, unless someone else here can help,

all the best!