Couple of MS? Going from LINK.
 

So I have hit the limits of the 1.6L in my car and need to find a good and affordable solution and the MSII looks like it will work. The car is running a 1.8L 94 bottom 99 head with a custom turbo setup using parts from the FMII BBB turbo kit. The turbo and intercooler and a few pipes we reused from the original kit. The 1.6L setup did around 250rwhp. I want to get 280 or close out of this setup.
These are noob questions I’m sure. Link to picture of the current setup are on my cardomain page.

1. Can the stock ISC be used?
2. What about the TPS the 1.6 is on or off. So how is this addressed? I also have a 99 and 04 TB and TPS I could use.
3. Can the MS drive Peak and Hold injectors? 650cc
4. Am I correct that the CAS can be used for timing?
5. What seems to be the best ignition coils setup? I want to upgrade the coil setup.
6. Anyone running a AIM wideband with the MSII? WB is in the car now.
7. Any other info or suggestions to help are welcomed.

You'll want to use the '99 TB with variable TPS. You can use the 1.6 TPS but instead of running TPS accel you run MAP based Accel enrichment which some say has slower throttle response for their application.
The CAS is used as your timing input.
I run an AEM Wideband with my megasquirt, it works great.
Megasquirt can control both low and high impedance injectors.
I use stock coils, though some upgrade to Neon or DSM coil setups, the DSMs are a more robust coil.
I can only suggest going MSI instead fo MSII because I use MSI myself as well as most of us on this board. There are 1 or two guys with MSII but we haven't gotten into it here.

mapdot accel works just fine, IMO. MS1 with extra firmware is what you want, MSII offers no real advantages at this point.
ms can run low impedance injectors, but you'll need to find better grounds than the OEM grounds, or you will get tach spikes.

See also: https://www.miataturbo.net/forums/showthread.php?t=9259

And http://www.madracki.com/miata/wiring.html

Looks like 2000 TPS pin-outs are the same as 94, except the 2000 doesn't have the Red switch wire.

-Mike