This may be crazy but I've been kicking it around and wanted some more opinions.  I've just come into possession of a Miata with a bad engine and a newer Miata engine with VVT.  The new engine can use the older ECU, but will lack the VVT functionality, and I don't have the newer ECU and key and the immobilizer would be a problem.

So I know our Bosch ME7 system pretty well.  And Bosch made a modular system so that it could be applied to any engine.  Also, the Bosch has plenty of resources to help with problems.  So it should be possible to set up the Bosch system to run any engine if you configure the inputs properly.  And then the Bosch is readily available and cheap.

Has anyone ever successfully used the ME7 system on a car it wasn't intended for?

You will need to convert to drive by wire (electronic throttle). You will also need crank and cam triggers that will work with ME7. Digifant cars are swapped to ME7 fairly often, which would be conceptually similar.