I tried to access the admin pages on the broken sites again but could not see these redirects
Oops you were talking about the SuperFish redirects. Forgot about those. Juggling 50 balls as usual. ha ha ha. Yep, let me know how it goes and since you are doing a manual install then what I suspect that you will find after you get back into one of the sites is you will see WordPress Core files in Quarantine. You can delete those files in Quarantine of course since you will be installing new WP Core files.