CEL light on tries to stall and making a clunking noise

If it is an automatic and you were charged for a clutch replacement I would be talking to the law, automatics do not have clutches.

However if you mean they rebuilt the transmission and replaced the converter because it was failing that would be different. It does have a lock-up clutch in it.

As to what is wrong? It could be many things, they may not have repaired it as well as they should have, or it could be something totally different. The CEL can come one for a multitude of issues, from a loose gas cap to misfiring cylinders, from a bad sensor to a bad engine. What it basically means is that the computer sees data that it thinks is bad, that data could be from the engine, transmission even something like a loose gas cap can turn it on.
The dealer tech will scan it, then try to determine what is actually wrong based on what information the code and other data tells him.

Okay, that vehicle must have the Powershift six speed in it. A lot of claims against it in the Focus due to the clutch packs causing shuddering and shift issues. Ford's current idea is to just keep replacing the clutch packs as they fail, with the same parts that failed. There have been reports of them failing in less than 6,000 miles after replacement.

Hard to say. Ford is acting like it is not an issue. Personally I would trade it in a heartbeat. The issue then is finding a replacement that does not have many issues. Sort of the devil you know versus the one you do not.

Maybe read up on it some more and understand the problem, then go in and see what Ford is willing to do to keep you as a customer. Maybe even go over the local dealer to Fords customer service and talk to them.