Everthing looks like it's back to normal. I can now access the task manager and no strange programs ask for internet access upon startup.

Thats great to hear.

I just have some follow up questions.

I'm still seeing a record of some strange programs in the program control tab of Zone Alarm. Can I delete them from Zone Alarm and use the HijackThis "Delete a file on bootup" feature to make sure that they are removed from the system?

Yup , you can remove them from that list. And you can indeed have a look if you still can find any of those files and delete them but they are harmless now anyway , and might not even be present anymore. Good change it was the same file just with a different name each time , or new randomly generated files.

Are my files safe? I have them on another partition (D), I just need to make sure that they are unaffected before I back them up.