Rough Idle and overheating

My 94 gradpix 3.4 suddenly started idling roughly I have had problems with over heating due to a possible bad temp. sensor. My main concern is the rough idle. My exhaust sounds wierd too. It kinda sounds like an old tractor or something. I have some guesses to what is cousing this, but i need outside input.

What does the exhaust sound like? Does it pop when the car is idleing. If so you may have an engine misfire or a burnt exhaust valve. The only way to see if the valve is burnt is to do a compression test. If you have a misfire you should have a misfire code in the computer. Scan it to see if there is a code and this should help you find the problem. If there is no code then do a compression check to see if you have a burnt valve.
If the valve is the problem the cost will be high due to having to tear the head off and either replace it or repair it. Quite time consuming.

After alittle investigation i now know that one cylinder isnt firing. Its not the spark plug or wires. Does anyone know which direction i should go next.

oh and it doesn't miss when i first start it in the morning and the exhaust does have a popping sound. I think my next step would be the coil, but i thought if a coil goes out 2 cylinders go with it? I could be way off. I've never had to deal with the electrical system. I am trying to learn as i go.