I think what you SHOULD have done is file the 1040X BEFORE you filed the 2553.  As it is now, when the 2553 was filed, they did NOT meet the requirement of the "entity and all shareholders reported their income consistent with an S corporation election".

As for what to do now, I don't know.  While filing the 1040X would support the intent, I personally don't think it is valid to do so.  Also, it is likely the the IRS decision for the 2553 will be done by the time the IRS processes the 1040X, so I don't think filing the 1040X would improve the case.