[PorkChop]

As said, it depends on what gearbox(es) you have available, what your intended use of the car is, your budget, how simple you want the build to be, what you fancy...you don't necessarily need to be limited by using an Emerald (or any other standalone) ECU and the possible expense of making it work with whatever engine you end up choosing. However, you do have the luxury of not needing to fork out for a standalone should you need to go down that route.

I'm on my third or fourth engine choice ATM, but my decision is partly motivated by what class my car would be in for sprints & hillclimbs whilst maintaining a sensible budget, plus what other running gear I have available.

The MX5 MZR engine (found in the Mk3) is the same as a Duratec and therefore a MZR gearbox would fit a Duratec. However, they are a different bolt pattern to mark 1/2/2.5 MX-5 gearboxes and AFAIK not interchangable. Mk 3 boxes still command a healthy premium, unlike 5 speed mark 1 MX-5 gearboxes, where they seem to be cheaper than Type 9 boxes.

The VXR engine is used in the Westfield Sport Turbo, with an MX-5 gearbox (I don't know whether an adapter plate would be required, but I'm guessing so). You're looking at a 4 figure sum to buy an engine from a breaker though, due to its newness.