" The Malwarebytes scan did take some time."
Did you run the "Full Scan" or the "Quick Scan"? If it was the former then it will take ages. The Quick Scan is dramatically faster as it only searches the locations where malware normally resides and is apparently 99.9% effective. Before I run a Quick Scan I use Disk Cleanup to delete Temp and Temporary Internet Files. The scan then takes a maximum of 15 minutes.
If you want to prevent your friend becoming reinfected, uninstall Java, replace Adobe Reader with a different PDF reader (such as Foxit), and ensure Adobe Flash is always up-to-date. If it's essential to leave Java installed then always update it the moment you're notified.