I am a computer scientist by day, and the most common issue we see causing computers to suddenly go ape is a bad power supply. An oscilloscope will quickly reveal that the +5 or +12 voltage outputs are noisy rather than flat DC voltages. But the interesting thing is that you typically don't get a machine that refuses to boot. It just becomes "flakey", sometimes infrequently, sometimes completely bananas all the time.
The alternator A/C to D/C conversion has to go right. Lights and stuff don't care. The computer does. And you can't tell with a normal voltmeter. A good one that can pretend to be an oscilloscope will show the DC output to be not so "DC" once you know what to look for.
Other things that will cause this include corrosion in the connector blocks where the wiring harness is disconnected to make it easy to remove the motor. Check it and make sure there is nothing but clear dielectric grease in there, no green gunk. Had that on an older 90 fox we used to run on the street/strip.