HELP Ford Ranger 1999 4x4 6 cyl auto real rough idol when in gear?

Anyone know what could be causing such an extreme rough idol when the truck is in gear---comes and goes when driving. My husband is currently deployed so although he could probably fix it I am left wondering what could be wrong and worrying about taking it in and it costing me a fortune just to find out what it is. Any ideas would be appreciated. Also, the check engine light goes on and off periodically--on for weeks or for days and vice versa. Thanks.