Whether the Trojan forked up Ad Aware,
Very possible.
I don't run AdAware these days but it always used to be good.
I just use a disk imaging program these days and keep regular backups of the OS. It takes 5 minutes to do both of my boot partitions and 10 minutes to recover from a completely hosed OS back to a known good image that is clean and fully operational.
I use this one I don't even have it installed on my machine I just use the CD I made with it to create and restore the backups.
http://www.disk-image.com/ I can't remember the last time I even bothered messing around with the system files or registry I'll just go back an image or two if things get messed up.