The 498a case cannot be withdrawn by her even if she is agreeing to not to pursue this matter any further.
In that you may have to file a petition under section 482 cr.p.c. seeking to quash the charge sheet before high court. She has to file an affidavit to that petition expressing her willingness to withdraw her complaint and she has no objection to this quash petition.
This may enable high court to pass an order to quash the charge sheet.
You can withdraw the RCR petition and file a mutual consetn divorce petition jointly on the basis of compromise arrived between you both.
Insofar as the settlement is concerned, you can draw a MOU agreeing to settle the amount and the mode of settlement and other conditions, which may be recorded in the MCD petition and the judgment.