The DiskPart CLEAN wipes all partitions - like a brand new disk again. If you are paranoid, do this before re-using the disk. I suppose if you were smart, you would NOT plug the infected drive into the laptop with your good data on it in order to do the wipe. Keep good and bad totally separate.
If the files are not encrypted, I don't think they can be infected. In fact even encrypted files are not infected, they are just encrypted. Do you own any paid anti-virus product? If not, you can get a free antivirus product and it can scan the entire computer, but you may have to ask it to scan a USB drive. It depends on the product. Some products, when you plug in a USB device, it will ask if you want to scan it.
I don't know what you mean about "email anti-virus". I suppose some email hosts will scan email for incoming viruses in attachments but I wouldn't count on that being the norm.
I think you are over-worrying. I would get all your data on a clean system. Install anti-virus. Scan all disks and flash drives. Then I would back up my data somewhere for safety. Then nuke the original computer and reload the O.S. Apply all Windows updates and then transfer your data.