Bizzarely I just fitted a VVT motor to my MK1 this weekend just gone.
be controlled by a MegaSquirt at this moment in time. You want either Hydra or Adaptronic for that.
The MK2 uses a FPR in the tank and two fuel pulsation dampeners one on the rail, one on a bracket on the intake mani. It's also returnless.
Unfortunately the MK1 FPR won't fit on the MK2.5 fuel rail, (well it will, but when you try to fit it to the head it fouls). So you need to either buy another rail, or figure a way to remote mount it.
MK1/2 coilpacks won't fit on the back of the head because of the VVT Oil supply. I've jerry-rigged mine to the top of the valve cover, but longterm have some Toyota COPS on order, Obviously if your motor comes with the MK2.5 coils this isn't an issue.
MK1 CAS fits the exhast cam like every other MX5 engine
MK1 echaust manifold fits like a glove, you NEED, (and want!) the MK2.5 intake manifold. MK1 Throttle body bolts right up so electrically (i.e. TPS and IAC) everything is fine.
If you have an early Oil Pressure sender (I retrofitted one to my 96) it'll foul on the rear starter motor bracket, (this is because the Oil feed for the VVT comes from the original OPG sender location, the new location is 2-3" lower). you can take some material off and it'll be fine though.
Other than that it's a straight swap really.
I blanked off the ports for EGR. and my (non USDM) VVT intake manifold doesn't have VTCS, but a simple RPM switch can control that.