Rough Engine in 1996 Lexus ES300

I have a 1996 Lexus ES300 with about 198,000 miles on it. Until this year, I had no major problems with the car. I serviced it according to the schedule in the manual. Then in March 2010 I brought it into the Lexus service center for routine maintenance and was told at the time that the (original) radiator was leaking and needed to be replaced. They showed me the radiator and it certainly looked bad. Then about two months later the car started having problems. When in drive, the engine was rough, both when accelerating and idling. The check engine light came on as well. I brought the car back, and the light code indicated a bad ignition coil. This was replaced. The car was fine for about two months and then the rough engine returned as did the check engine light. When I went back to the Lexus dealer, they were less sure about the cause of the problem. They said it was possibly (1) a small hole (or holes) in the radiator hose in the engine; (2) a stuck valve; (3) a cracked head gasket. Since the car did not exhibit the signs of #3, I am more likely to believe it is 1 or 2. The engine goes through cycles. It is fine for a few days and then becomes rough while in drive. Even when it starts out as rough, it is not as bad when the car warms up after several miles. My question: is there a straightforward explanation of the problem?

I serviced it according to the schedule in the manual. Very Good! Although I would recommend changing the transmission fluid (assuming automatic transmission) every 30-40,000 miles.

I brought it into the Lexus service center for routine maintenance Generally they will provide good maintenance, but so would a good independent mechanic and the independent will charge a lot less.

the light code indicated a bad ignition coil. codes indicated a possible problem with the ignition coil.

[i]  They said it was possibly (1) a small hole (or holes) in the radiator hose in the engine[/i]  Have you been loosing radiator fluid?  Has there been any indication of the engine overheating? 

[i] a stuck valve; .. a cracked head gasket.[/i]  

That sure is a wide range of possible problems. Unless you have been loosing coolant (radiator fluid) I would rule out #1

I would recommend finding a local mechanic, ideally one who has Lexus experience.  Your dealer does not seem to be the best of Lexus dealers when it comes to service.

How long ago were the spark plugs changed? This motor may have multiple ignition coils, and another one could be going bad.

#1 doesn’t make any sense.

#2 is so general that it really means zippo.

Basically the dealer is saying they have no clue and their guesses are wild guesses.