After both parties have signed separation papers and we are at65 days after filing, can he now contest what we both agreed to?

Well it depends on what type of “separation papers” were signed. If you entered into a CR2A agreement the answer is most likely no. However if you both just signed the final dissolution papers and are waiting for the 90 day mark to have them entered then yes he can object if a few things are done. If he signed the joinder to the petition but did not file the response then he will need to file the response. If he filed the response to the petition then you both agreed on the final papers and he no longer agrees then he can pull his signature from the final documents.
You may want to consult with an attorney, many offer 30 minutes free, to get a better idea of your rights as there are a lot of unanswered questions regarding what type of separation papers, if those papers were signed by a judge, if someone signed a joinder, if there was a response to the petition. Any answer yes or no to the above results in a different outcome.
I hope that helped some.

The answer depends on what type of separation papers were signed.

If you were both represented by counsel, and you and your attorneys all signed a CR2A agreement, it is almost impossible to change the terms of the agreement.

If you both signed a Separation Contract without the advice of counsel, or you both signed the final Divorce Decree outlining the settlement terms, then your spouse can request that the court NOT accept the agreement.

I would contact an attorney if you have not yet done so.