1995 Jeep Cherokee RUNS LIKE CRAP (SOMETIMES!)

My wife and I have a 1995 Jeep Cherokee Sport with the 4.0 inline 6 cy.
Sometimes when you get in and start it the thing runs like only 5 of the six cylinders are firing. However, We can stop, go in Kroger, come back and start it up again and it runs fine.
We have replaced the fuel filter, plugs, and fuel pump. I have disconnected the CPS connector and reconnected it, (advice from another forum), and had a look at the throttle body, (did not really know what to look for). The fact that it only mis-fires sometimes is very confusing. When I checked the diagnostic codes using the check engine light method, the first code given was 55 signaling the end of the test.
Can anyone help or advise me about what to do? Thank you, Tommy