Ghost in the engine?

I have a 1994 Jeep GC 4.0. Put a 1996 engine in it 8 months ago. Since then, I drive down the road for a few miles and without warning, it dies. I wait about 20 minutes, it starts and may drive ok for weeks. Then it will start the pattern all over again. I've cleaned the fuel injectors. The problem persists. If it were the fuel pump, wouldn't it stay stopped? Seems whatever it is has to "cool down". Also seems that something gets "clogged" and has to be released. Anyone have any ideas. The auto "experts" can only figure it out if it's attached to a computer while "broken down". I can't make it break down on schedule. Thanks!

2 things come to mind. The Ignition Coil is going bad and starting to overheat. OR The Fuel Pump is going bad and starting to overheat.

Both os these are known to overheat and cause the vehicle to shutdown and then you will have to wait for them to cool down before they will allow you to restart. From your description it sounds more like the FUEL PUMP, the FUEL PUMP will overheat when you get below half tank of gas - at this point the pump is not fully submerged in fuel wchich helps keep it cool. Have you noticed the FUEL level at any of the times it shutdown?

same think happened to me before,changed crank saft position sensor that was it