I personally did this way:
Uninstall root totally from SuperSu app itself.
Let BusyBox as is.
Flash the original boot.img of the rom with TWRP.
And then you can flash Magisk or Phh SuperUser choose what you prefer.
You go to Play Store and install BusyBox Stericson app to manage BusyBox and you're done. It's unnecessary flash the rom , but you can choose if you still prefer.
---------- Post added at 07:45 PM ---------- Previous post was at 07:42 PM ----------
when you say "reflash the stock boot.img" you mean restore a nandroid backup from a backup made by twrp ??? or a boot.img downloaded from somewhere?
When you're in TWRP there two options flash zip and flash image.
You choose image, so TWRP "ask" you if it will be for boot or recovery. You will choose boot and then swipe to flash and you're done . That's is all.
---------- Post added at 07:59 PM ---------- Previous post was at 07:45 PM ----------
@jam66 After you uninstall root completely from device you need boot.img because when installing SuperSu it patches the kernel. So to avoid problems with it, it's preferable to flash the "virgin" boot.img of the rom you're using. This way you will get a clean flash with the Superuser zip of your choice.