Some pointers about donor choice, or things to look out for if you're buying parts piecemeal rather than a complete donor.
All the 1600 and 1800 parts are interchangable to an extent. For example, you can run a 1600 engine and gearbox with a 1800 diff. You would need a 1800 prop and drive shafts to suit the diff. A 1600 engine will fit a 1800 gearbox.
Apparently (I don't know if this is true or not) but the 1600 gearboxes and diffs are slightly weaker than their 1800 counterparts.
A common upgrade for the 1600 engine (especially if tuned) is to fit the 1800 flywheel and clutch.
You can tell the 1600 and 1800 apart by looking at the cam cover - the 'Mazda 16V DOHC' lettering is raised on a 1800, sunk on a 1600. The 1800 has 'BP' cast into the block on the exhaust side.
The 1800 comes with bigger brakes as standard all round. Mark 2 Sport brakes are bigger still.
Early driveshafts are bolt on (and the PCD is different between the 1600 and 1800). Later driveshafts are push on (and I believe are still different between the 1600 and 1800).
There were several wiring revisions over the course of the mark 1's life.
Early 1600s ('short nose') engines had crank problems. Later long nose engines are fine. They can be identified by counting the number of slots on the crank pulley. The short nose has 4 slots, the long nose 8.
Any imported (Eunos) 1600 engine will be 115bhp, as are UK engines of the same era. The JDM 1600 was discontinued when the 1800 was introduced. The UK 1600 was then detuned to 88/90bhp at this time, so any later UK spec 1600 would be the 90bhp version.
The OEM alloys are very light for an OEM wheel. You would need to spend a significant amount of money to get lighter aftermarket ones.
A mark 3 MX5 gearbox will fit the Ford Duratec apparently
The mark 2 6 speed box is rumoured to be stronger than the mark 1 5 speed.