Well thankfully I backed up the first IPS4 upgrade MySQL DB and I just simply copied the two tables that I had the issues with (ips_core_notifications and ips_downloads_reviews) and the upgrade script went through without an issue. Also the theme issue has completely gone! Whether this was because of removing the plugins first or because I was using the newly patched IPS4 build I don't know, but my site is now back online and working.