I present to you: Now into reconfiguring Frankenso to run MAP with Speed Density (sounds soo freaking cool!) and accept the stock Miata wiring (atleast for '89 to '93 1.6, but later 1.6 Miata's are very similar):



Jumpers to set, use a wire for high current signals, a 0-Ohm resistor for low current signals:
Wire side - board side (Wire as jumper or 0-Ohm resistor)
W2 - W2 (power, obviously needed

W5 - W6 (This is for the check engine light, optional and I haven't checked if it works yet,resistor)
W7 - W7 (Ignition, resistor/wire)
W8 - W8 (Ignition, wasted spark so only two channels, will get into that, resistor/wire)
W10 - W57 (Only if you have A/C, don't know why I did this, I don't have A/C)
W18 - W35 (Cooling Fan)
W21 - W48 (This goes high when lighting is on, can be used to increased idle in the future, not used at the moment)
W39 - W39 (ground for the injectors, big wire)
W40 - W40 (ground for other outputs, big wire)
W41 - W41 (ground for ECU, wire)
W42 - W42 (ground for sensors (do not used this line to sink current!), wire)
W43 - W43 (Cam position sensor, resistor)
W45 - W45 (Cam position sensor, one is crank one is cam, will get into that, resistor)
W47 - W47 (An igniter output (driver of the coils), not configured and not used (yet?), resistor)
W49 - W49 (Power for the AFM, if you remove the AFM you don't need it, resistor)
W50 - W50 (TPS, make sure to convert to a linear type TPS, stock is just a switch, resistor)
W52 - W52 (Oxygen sensor, for maximal engine power and also safety convert to a wideband, resistor)
W53 - W53 (AFM output signal, if you convert to MAP don't place this jumper, resistor)
W54 - W54 (AFM IAT(intake air temperature) signal, if you convert to MAP make sure to place an external sensor near the throttle body, resistor)
W55 - W55 (CLT sensor or Coolant temperature sensor, resistor)
W59 - W59 (Injector 1 & 3, batch fired, wire)
W60 - W60 (Injector 2 & 4, batch fired, wire)
W61 - W61 (Idle speed control, wire)
W62 - W62 (opentional, I'm going to use it for the electronic boos control, wire)
I promised above that I would go into wasted spark, what it is, what it does and what you have to take into consideration. Wasted spark means that you have 1 coil per 2 cylinders, firing both cylinders twice in two rotations (four stroke engine, so one cycle is two rotations). That means that even though one spark is needed per cycle, the system fires twice. Sounds illogical right? Well, it is, sort of. It has to do with cost of manufacturing, as you might imagine, two coils are cheaper than one. One of the two sparks per cycle is lost in the exhaust stroke, so it doesn't do anything, but due to the low pressure in the cylinder (the exhaust port is open), it does not cost a lot of voltage to trigger the spark. Out of the +-15 kilovolts the system generates around 2 to 3 kV (kilovolt) is lost in that cylinder, that means that there is still 12kV left for the cylinder that is at the top of the compression stroke! (I'm making some assumptions, but this is the basics)
So the manufacturer (Mazda in our case) can save two coils and it doesn't hurt anything, performance is pretty much the same. There is one downside, due to everything working twice as much as needed in the ignition system, stuff like spark plug wires and the plugs themselves wear around twice as fast as needed. That is one of the reasons why our cars are known for eating spark plug wires. Mazda doesn't care, means they can sell you more spark plugs and wires.
But to make it work we obviously have to configure that in Tuner Studio, though it's very easy. You go to Engine, Base Engine Settings and set Ignition Mode to "Wasted". Now for the Cam signals, remember I said one is for the crank and one is for the cam itself? I hear you thinking, but I only have one sensor, the CAS? Correct, but it has two profiles inside, so it's actually two sensors in one.
For the signals themselves you have (or you should have) already soldered the 0-ohm resistors or wires in place, but a bit of reconfiguration is needed.

You may ignore the top orange wire going from 5V to the resistor, it's the horizontal one.
The two important wires are the ones with one of the sides near the opamp, and the other two sides next to each other above the right side of the opamps. These op amps buffer the input signal from the hall sensors so their outputs should be connected to the inputs on the discovery board, in order to get the trigger signals through. Solder both wires in place and remove (or don't place) R315 and R295, these form a divider with two other resistors, and lowered the level enough to make the discovery board miss the signal. If you remove those two the input is high enough for the discovery board (might actually be to high since it is 5V, will do some checking out but has worked for over a 100 miles for me).
I've uploaded my TS project, should be good enough to get it started but it is MAP with speed density, which I will come to in a couple of days (or a bit longer if I forget it again, sorry Andrey!

By the way, for the high-low drivers (the four chips near the power supply), on the bottom make sure to connect all of their power supplies with the 12V line. You can just solder a jumper between VP and 12V on P604 to P607.