Installing Mojave with the patcher is an integral step of using the patcher but you have not done that. (Well, not clear whether you have)It doesn't seem like it's possible to boot a MacPro 3,1 from APFS using dosdude's Mojave Patcher, ... So frustrating.
If not, you need to rectify this omission.
In other words, install Mojave on a different disk following the instructions on the DosDude website and then transfer your data across.