Some things that can go wrong.
If wire R6 (althernator output) contacts any J2 or J3 wire, the engine will keep running. R6 is always hot because its connected to the battery.
If J1 (power to key switch) shorts to J2 or J3, same thing.
Shop manual has the full wiring diagram. The diagram above is just a schematic of the main circuits of interest
I have what looks like a fat pen with a metal tip with a angled groove that fits on the plug wire. All ya have to do is lay it on the plug wire and it'll flash a small light if there's juice running through the wire. Super easy to use.