Took me a bit to realize that Grbl5... is not Grbl L Mega. I want to use GrblGru for threading, and just woke up to the opening statement - the two aren't the same.
Looking at the pin assignment for both, there are some differences. Grbl 5 step a0 a6 D46 / or pins 22 28 and 46 on the 2560 board.
Direction bits are A1, A2 and D48 on 5, but D23/23/48 on L. Grbl L Mega pins are programmed so that all STEP are on one port, All DIR on another.
But 5 is set up with Z step and dir on different ports, Port A for x and y, D for z.
As I'm only using the two axes, formally X and Z (cross slide and long axis), I decided to remap the pins in L so that
X is now A0, Y is A6 (pins 22 and 28) for steps, and
X now A1 Y A2 for DIR. (pins 23 and 24
About to try this shortly, but the EN pins are not compatible with this approach, as X is on port D; Y and Z are on Port A.
I will come back when I've tried it out.