Mount the coil upside down.
If you make your pickup 180 degrees out it also has the same effect as mounting the coil upside down.
Your now running with crazy, the key to the entire thing is pretty simple you want to fire on alternating coil packs. In a 6 cylinder you just add a third so coil pack 1, 2, 3, 1, ,2, 3.
V8
1,2,3,4,1,2,3,4
V10
1,2,3,4,5,1,2,3,4,5
V12
1,2,3,4,5,6,1,2,3,4,5,6 or 1,2,3,1,2,3
Dual plugs you just run multiple coil packs in redundancy.
1a&1b,2a&2b, you get the idea.
This is all wasted spark setups, once you go with sequential, things get so much easier

Then you have to figure out the logic to drive the coils in the order you want them to fire. I am now taking this beyond your question and sorry for that.
Maybe I should do a mini school on EFI logic, and wiring. We are getting into so many engine combinations it is not longer just a discussion type-IV, and -6 engines. Even -6s with twin plugs makes things just a tad worse. Luckily your Subaru 2.2 is about as basic of an EFI engine as you can get, so a MicroSquirt unit should be pretty simple. Being said we have not gotten into doing anything the EFI input sides.
Back off my mad ramblings the firing order of the engine 1-3-2-4.
In your drawing you have the order correctly as that is the firing order, but your cylinder numbers or as I called spark plug is not.
1 in your drawing is cylinder or spark plug number 1 hook it up to coil side 1/4
2 in your drawing is cylinder or spark plug number 3 hook it up to coil side 2/3
3 in your drawing is cylinder or spark plug number 2 hook it up to coil side 1/4
4 in your drawing is cylinder or spark plug number 4 hook it up to coil side 2/3
Makes it any clearer than the mud it is?