Hyundai Repair: 2000 Hyundai Tiburon wont start, hyundai tiburon, initial scan

Question
OK, my wife has a 2000 Hyundai Tiburon, and the other day she tried to start it, and it would crank but wouldn't turn over.  She tried and tried, and eventually called AAA to come tow it.  As soon as she did that, she tried it again, and it started up, but then she noticed the check-engine light was on.

AAA came, and said it had to go to the dealer, because they didn't have the right equipment to diagnose it.  When the dealer looked at it, they did one diagnostic test on it, and couldn't find anything.  They called my wife and asked if they could do another diagnostic, and she said alright.  They originally thought that it was a number of different things...  First, they said fuel pressure, then they said something about the ignition timing, then they finally settled on the ECM.  She said they took everything apart, and figured that that reset the ECM, because the check-engine light went out.  She took the car back, and 2 days later, it wouldn't start again.

So, now it's at the dealer, and they ordered the ECM, and she said it would total about $1200 for everything.

My concern is:  Is the dealer the only place to get this done?  Are they overcharging?  Is there someplace that is possible to have this done cheaper?  Is this even the right part to change, or could it be something else?

Few other things:  She said there was plenty of gas in it.  She didn't say if it cranked fast or slow.

I'd really like some help with this, because she's getting very frustrated, and there's not much I can do, since I'm deployed in the Air Force right now to Iraq.

Thank you for any help you can give.

Answer
Did the diagnostic test run by the dealer include an initial scan for diagnostic trouble codes?  If so, the trouble code will provide the best information regarding where to start looking for the issue.  If I know the code, then I'm in a better position to advise as to the potential correctness of the dealer's diagnosis.  If the ECM is unplugged, it will erase the trouble codes, making the problem more difficult to diagnose, nearly impossible if the problem is not occurring when the diagnosis is being done.  A faulty crank sensor would be a much more frequent issue than a defective ECM.

I do not think the dealer is overcharging.  The ECM is an expensive component.  Whether another place would do it cheaper is hard to say without calling for price quotes.  And you'd need to include in your analysis any diagnostic fees you'd need to pay the dealer for the work they've done thus far.
May you have a healthful and speedy return to the U.S.