Boyer wiring
the red wire from the boyer
... should be connected directly to the battery +ve terminal. It is the supply to the "Transistor Box" electronics, they only draw about 250 mA so essentially there must not be any resistance between battery +ve and the Box; connecting this Red wire anywhere other than the battery +ve terminal increases the possibility of resistance in additional but unnecessary connections, or resistance developing over time.
the red wire to the frame from the coil
While this is what is shown in the Boyer fitting instructions, it is poor in practice.
Any electrical circuit starts at battery -ve and ends at battery +ve:-
. as standard on your bike, the ignition circuit is from battery -ve through the ignition switch and kill button;
. Boyer fitted, the kill button White/Yellow wire is connected to the Transistor Box White wire, the Box Black wire is connected to the coil (should be coil -ve);
. coil +ve to battery +ve, there is no useful purpose connecting the coil to the frame and then relying on a random connection somewhere else on the frame to battery +ve

- as with connecting the Box Red wire anywhere other than the battery +ve terminal itself, this increases the possibility of resistance in the additional but unnecessary connections, or resistance developing over time;
. I always connect coil +ve either directly to the battery +ve terminal or at least to a nearby harness Red wire - as standard, all harness Red wires are connected to battery +ve.
The black jumper from the coil was attached to the same terminal as the red wire to the frame.

You are lucky that did not toast the Box.
The original pair of coils has been replaced with single one with two HT leads? If so, it is possible the coil LT terminals or wires are not marked -ve and +ve, wiring convenience or best guess.
since I can't even seem to remember where I put my coffee cup who knows?
If you connect either both Box and coil Red wires to the battery +ve terminal, or the Box Red wire to the battery +ve terminal and the coil Red wire to a harness Red wire, reduces the possibility of later mistakes.