Another question - Did you perform the dynamic test of the alternator output from each of the three stator coils? This is done with the engine running and seeing what voltages are coming out of each of the three yellow leads from the alternator.
Those voltages should all be within a volt or two of each other. If one was low, that means a bad winding, possibly the varnish between the wires on that winding melted causing not a short to ground, but an isolated short in the winding creating a lesser voltage output because you have fewer INDIVIDUAL windings in that coil, with possibly many unvarnished windings having made connection. This would not show up as a shorted to ground problem at all and could only be detected by the dynamic test. Possibly the resistance check of each winding would pick this up also.
This is what apparently happened to my stator in my previous '95 model. I had no continuity to ground on any stator winding, but two were putting out 25V and one was down to 18V. In that state, I was still able to get sufficient voltage to the battery for charging (just over 13V somewhere), but only with the headlight fuse pulled.