The first question that springs to mind is how late is the PM in providing his asessment on your CE submittal? Is he indeed assessing the CE in line with the time scale provisions of cl 61.4 ? Did you give him notice of his lateness and agree to an Extension of time for his assessment?
The assessment by the PM has to be made and based on the submittal you made. If it is not, then the PM by all accounts is making his own assessment as per cl. 64.1 . In doing so, he is obliged to explain why he feels obliged to do so. This is very dangerous ground for him to tread for he must justify his Action through one of the four given bullet Points therein. Failure to do so and moreover, if his reasoning is not 100% accurarate, lends him liable to lose in a subsequent adjudication.. An assessment by the PM really only gives you this one option of adjudication - note however, the time Limits for notification.
You mention a resubmittal which presumably the PM may ask for, based on the newer accepted Programme.? This is definately a no-no. The original CE notifiation must have stated particular criteria upon which the contractor's Quotation should be based and the then currect accepted Programme ( or the contractor's submitted Programme) in the CE Quotation) is the valid document.
The "over estimations" you refer to are no doubt meant to reflect the provisions of clause 65.2 where such a forcast, if subsequently shown to be wrong cannot be revised. However if the assumptions on the Programme activities were based on assumptions provided by the PM at the time then he does have the right to notify a correction subsequently through CE 60.1 (17). but this must be a separate exercise, no matter how appealing it may be to lump it into the same one.