Ok no problem you can use a jumper from L1 to L3 in front of the breakers, this schematic shows how the 2 Transformers are wired they use L1 L2 L3 for there supply power , by connecting this way everything with the wiring of the machine stays the same, no jumpers needed anywhere only at the power input
You can continue to use it the way you have and just add the Jumper at the VFD drive R to T
The way I suggest you don't need your Green jumper or the one at the VFD
Connecting L1 to L3 with a Jumper takes care of all the power requirement's
Mactec54