Overpaid CMS by thousands...

CMS don't pay your wife up front and then claim it from you so there is no reason they would do the same in reverse when you overpay. You are in the same situation your wife was now but in reverse as she owes you. Look at the situation, swap the names around and substitute 'CMS' for 'Court':

Tell your Ex she owes you this and you want repayment over x term.
Ask her to agree this with you directly to avoid including the [STRIKE]CMS[/STRIKE] Court
IF she does not agree then make a claim via the [STRIKE]CMS[/STRIKE] Court
[STRIKE]CMS[/STRIKE] Court Will (hopefully) order her to repay and set some terms
If she does not stick to them then go back to [STRIKE]CMS[/STRIKE] Court and ask them to enforce.

The only difference you have here is that the Court do not do this for free whereas the CMS do. Any court fees can be added to the debt if it is agreed she owes you it, you should make her aware of this at some point.

It is infuriating but try to look at it this way.. For a lot of parents there is minimal access to the courts to secure unpaid child support, the CMS basically fill that void. I have been both a payer and a receiver with the CMS before and I hate them just as much in both cases... Their system seems arbitrary and always in favour of the receiver, whatever the detriment to the payer would be. The courts do not work the same way and will be more human in resolution. This may not be ideal when you are wanting your ex to experience what they have made you experience but it is the justness of our legal system that sets us apart from other countries where you are able to destroy someone through the courts at will. Maybe it would be nice if you couldn't destroy someone through the CMS also...