Not Sure, But May Be An Electrical Issue?

My 1993 4cyl. manual trans. Wrangler runs fine but intermittently bogs down or even shuts off. Immediately following this issue I get a knocking noise coming from the motor. Within 5 minutes my power is back and slowly (20min - 2 days later) the knocking noise will go away. Is there something in the wiring that would cause this? I have had a complete tune-up and replaced the crankshaft sensor with no results. All ideas are welcome.