The contract requires the project manager to retain delay damages when assessing the amount due after the completion date, see clauses X7.1, 50.2 and 51.2. The client can, of course, pay more than you have certified if they wish. We would therefore suggest you think very carefully about this, as you will, in effect, be breaching the requirements of the contract.
If, for example, you were employed under an NEC4 Professional Service Contract (PSC), it could be argued that you have not used the skill and care normally used by professionals providing services similar to those you are providing (see clause 21.2 in the PSC).
As for the waiver issue, that is a legal question and you would need to seek legal advice on this.