Thanks for the comprehensive feedback.
If you do decide to enable Falcon again and you see these symptoms, it would be very helpful if you could share your .htaccess file with us before you restore the backed up version. I'd like to see how Falcon modified it and what else you have in there that may cause problems. That way we can build in compatibility for your specific scenario. You can email your htaccess to genbiz @wordfence.com if you do decide to try this in future and we'll investigate.
Thanks.
Mark.