Ideally, you would run a standalone ECU like Megasquirt to fully utilize the ITB's capabilities. The ITB's are 42mm ID throttles from a 1000RR Honda (see? you get SOME honda parts, lol)
However, with a plenum - you can still route all the airflow through the VAF. A TPS adapter would be easy to make. There aren't any complicated linkages to make for the throttle cable - you can use what's there.
The nonturbo Capri uses a B6D engine - basically a turbo-less B6T. Higher compression, slightly different cams, different ECU. Running a Miata ECU isnt worth the huge hassle it would warrant - Megasquirt would be best. The 1.6 Miata stuff isn't really tune-able as far as I know.
The IAC/BSP is an independent unit, and as such you can mount still run it. You'd probably end up with a vacuum block from each cylinder for sensors, the IAC could attach there.
This ITB manifold was designed to fit the Miata as well
I've made a water bypass plate to go with the manifold - it's a spacer that sits between the thermostat housing and the head. You need longer bolts for it - but it moves all the coolant fittings away from the manifold while still keeping proper pressure differentials in the system to make things like the heater core work. You can also put the stock temp sensor into it.
I haven't looked, but I'm sure someone makes phenolic spacers for the Miata - they'd work on the Capri. The Miata doesn't use much water in the manifold though, just some for the IAC valve - the Capri uses quite a bit so you'd want to delete that.
Here's FE3 info + the stroker build:
http://www.solomiata.com/FE3.html Lots of really, really good Mazda engine info on the rest of the site so look around!
I can say with relative certainty that you won't be able to fit a double A-Arm suspension in the front of the Capri without some really major surgery. There's just not enough room. It's designed for the Macpherson strut+lower control arm combo and not much else.
And by "Massaging" I mean I had to take an oxy-acetylene torch and plasma cutter to the subframe, and then weld in 1/2" custom bent reinforcing bar around the new drivetrain
Where are you located, it's not in your profile. I have an extra rust free subframe for sale if you're interested.
You can look around for an old PaceSetter header for the Capri - they were made at one point. Now you either go custom, or adapt something else to work. Some of the Honda's have almost identical port size and spacing on the exhaust size, you could re-drill the flange to work or weld a new one on...lots of options there
Sorry for the unorganized blobs of text, lots of questions to answer and I've been up a while