I looked through our entire post and I don't see where it would tell me if I had a Trojan or not. Should I assume that I didn't?

We removed couple of them through Combofix, so, yes, you did have them.

After 12 1/2 hours, I closed out the defragmentation because I wasn't sure it was really working. Should I try it again?

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I'll mark this thread as resolved.