Travelling problems

i have a 91 explorer when i take it on long trips about 2 hours into the trip my check engine light comes on and then it goes off and so on for the rest of the trip also sometimes when this happens when i come to a stop and rev back up again i get a clanking sound for the first little bit then it goes away ive driven the car 8000 miles since the first occurance and it happend again another time but after the car rests it goes back to normal. any ideas or thoughts on this would be greatly appreciated thanks you