I took some measurements and pics of my MSM manifold today. It should be the same as 2001-05 VTCS manifolds on USDM cars.

I also measured ID and OD inlet and outlet of the MSM throttel body which is probably the same as all Miatas.

Some data for MSM manifold:

Plenum volume: ~ 1.1 l
TB inlet: 59 mm
Runner diameter: 42mm
Runner length: ~31-32 cm
Weight: 7.3 kg (With EGR valve, no TB )

JDM manifold: ( from my earlier post )

Weight: 6.4 kg
Throttle body opening diameter: 59mm
Runner diameter: 50 mm
Runner length: ~ 30 cm
Plenum volume: ~ 1.5 l
Calculated runner volume: ( 3.14 * sqr(2.5) * 30 ) / 1000 = ~ 0.59 l each

OD inlet 66mm
ID inlet 62 mm
Throttle plate / ID outlet 55 mm
For dummies: The Miata TB is 55mm. NOT 62mm.

Lets look at some differences between the MSM and JDM manifold. JDM on the left:

I need to tap for vacum for the MAP on the JDM as it has at least 1 port less.

Looks pretty similar from the other side.
Plenum looks shorter on the JDM manifold but if you compare with the runners they are pretty much the same width.

Underside looks the same. Hopefully the manifold brace from the MSM will fit.

No obvious changes from this angle. EGR fitted to the MSM manifold and you can see the holes from the removed VTCS shaft.

TB inlet has a more straight path and less restrictive bulges and holes on the JDM manifold:

On closeups the difference is very noticable:

JDM manifold has 50 mm runner diameter vs. 42 on the MSM.
Also the MSM manifold has a strange second chamber between the runners and Helmholtz chamber. That could mean the Helmholtz chamber on the JDM manifold is bigger.

The runner outlets on the JDM is connected to the Helmholtz chamber via small 1-2 mm ports in runner 1-3. MSM does not have these:

The runners protrude about 1 cm more into the top part of the plenum on the MSM.
EGR outlet is also bigger.

I'm finishing off with some pics of the throttle body:

So... Which is best ?
You really don't know without a dyno or a flow bench as fluid dynamics stuff is a very complex subject ( I have been told...)
However it is hard to not notice the straighter flow path and more open design on the JDM manifold. The plenum and runners are larger wich could be a good thing for overboosting.
I would also think there would be better gains of fitting a larger TB as the air doesn't have to smash into a couple of 45 deg walls before entering the chamber. No restrictive VTCS butterflys or holes to weld if they are removed.

In my head the JDM manifold is better.