Hi there Tim! I did do all the steps in the guide. I had Wordfence clean out both Wordpress blogs that I run, both of which were hacked. :(
I think they must have a backdoor or something, and maybe it's interfering with Wordfence being able to detect malicious files.
Last night my server was apparently used for a brute force attack! And my server has since been shut down. I'm working now to try and migrate my files out (the one step I didn't follow in the guide was backing up!) and fire up a new server, this time more secure!
Thanks for your help. I think maybe by the time I had Wordfence installed it was too late, my site was too compromised.