This sounds like you have a bad connection some where. Make sure the cable and wires on your starter and battery are good. Actually take them off to check them out.
Hi, sorry to jump in here, am new :) I had the same problem and after all the checks and money spending, changed the starter and now she starts like a dream. Hope it helps.
I have had this problem in my 94 wrangler and you will find that the colder it gets the longer it will take for the check engine light to come on. I have fought with this for a year spending money with garages and so I decided to replace the computer (about 300.00) and now it is like brand new. Starts right up and runs better too. I did change the computer myself and it took all of 15 minutes. It's located on the firewall under the hood on the driver side.