Working from memory, you have essentially a combustion event every 180 degrees, alternating between the rotors, and advancing one face of the rotor each time.
So 0° = rotor 1 face 1, 180° = rotor 2 face 1, 360° = rotor 1 face 2, 540° = R2F2, etc.
So instead of 1-3-4-2, it's R1F1-R2F1-R1F2-R2F2-R1F3-R2F3 for the order.
One "cylinder" takes 1080° instead of 720° to complete an ICPE cycle.
Because of this, you can pretty much fuel it like a regular four cylinder engine, since you still have an intake event each 180° of shaft rotation. Just set it as twice the displacement as far as fueling is concerned.
There are primary and secondary runners with their own injectors, and primary/secondary throttle plates that correspond to those injectors.
Only the primaries fire till the secondary plates start to open, then both fire. Batch firing seems to work OK, sequential also works. Depends how flexible the injection can be.
At 3800 RPM, the auxiliary 5th and 6th intake ports open to allow more charge volume into the engine. Fueling is adjusted in the maps based on the known actuation point.
At 5200 RPM the VDI (variable dynamic intake) kicks in, and shortens the runner length for top end torque.
Both of the intake port systems are solenoid controlled.
Ignition wise, it's rotor 1 leading, rotor 1 trailing, rotor 2 leading, rotor 2 trailing, ad nauseum.
You have 180 degrees between leading plugs, and the trailing fires between 0 and 15ish degrees after the leading plug, depending on how you dial things in, load, phase of moon, and if Elvis has been sighted on the drag strip. (Sorry, joke had to go someplace.)
On the stock system, there is one leading coil that fires both leading plugs at the same time in waste spark, and a trailing coil that has two inputs, select and fire. Select chooses the rotor, fire fires the selected rotors trailing plug.
The RX-8 uses 4 individual coils, but they are quite a crappy design compared to the old setup. The change from 2 coils was made for cost reasons and packaging concerns.
A four coil system can be made with GM D585 coil packs or RX-8 packs.
Idle timing is around 20°ATDC for face 1 rotor 1, advancing up to around 30°BTDC at max rpm.
I ended up consulting the megamanual, rx7club, and another site found by google search for ignition timing information, since that part was hidden behind a missing synapse in my brain.
mega manualcoil and additional timing diagrams