Thank you for that link,
@internetzel
Interestingly enough, I found a similar process in the following YouTube video
However, even following those steps to the letter, I still got the same error when trying to boot from my hard drive. I then booted into the Mojave Patcher USB boot disk to see if I could select my internal drive as the startup disk (before following the above process I was unable to select it without an error). This time I was able to select it as a startup disk, but when it booted up I got the same terminal boot screen with the verbose output resulting in the same error "Boot file not found, exiting..."
So I bit the bullet and erased my drive and reformatted as HFS+ again and now am in hour 5 of a 14 hour restore from Time Machine Backup
Other than following the steps listed at the URL you posted, did you have to update your MacPro 3,1 EFI via some installer/updater? My gut tells me that unless I'm able to update the EFI I probably won't be able to use APFS.
On a related note, have you noticed any benefits of using APFS over HFS+? If I'm not going to get any performance/stabilty benefits I may just convince myself to stick with HFS+ and not jump through any more hoops.
Thanks again!