What 1492 said, plus some random thoughts:
If there is malware on your computer, any USB device (drvies, printers, camnera, etc) can pick up the malware. If you backed up your files, the malware is on the backup drive also.
Windows restore is a common place for malware to hide. Most AV scans don't look in there or don't do a good job looking in there.
The PUPs are usually benign programs that are either useless trialware or shoddy cracking software. If the OP still has the names of the PUPs he should run them through "hijack this".
It's easy to say "don't click on an email you're not expecting", but a common form of spearphishing is a bogus UPS or Fedex notice. Very tough not to click on that if you're impatiently waiting for a Fedex.
The email is mostly likely nothing or most likely was caught before it did anything. And I would be reassured if the PUPs were all Malwarebytes caught--it is the best MANUAL scanning tool available.