Maybe your water leak is leaking on your alternator/electrics or engine management sensors.
Clean all the sencors up and check them.
Another idea is when its idling push and pull slightly on the inlet manifold and see if that effects the idle as a buggered inlet manifold gasket can cause those rpm symptoms.
Also Connect your s12 to another car with jump leads with the other car running and see if that helps as 12.5v is not enough output at the battery with the engine running.As you say it should be ok but i dont know how fussy your management is
oh..and.........3000gt are big and heavy lol
