The instruction from the Project Manager is a compensation event under clause 60.1 (4), so this should have been notified by the PM at the time of giving his instruction. If the PM did not notify, then the Contractor may notify the matter as a compensation event which the PM is required to respond to.
The above issue doesn't seem to be a matter for which an early warning would be appropriate, as when the PM decided to instruct the Contractor to stop work, this is a compensation event. If, however, it was a matter which the Contractor could (and should) have notified as an early warning, then the PM can notify this at the time of instructing the Contractor to submit a quotation. The compensation event is then assessed as if an early warning were given. This essentially stops a Contractor from withholding information to his advantage, and to the detriment to the Employer, as there may be appropriate mitigation measures which could have been taken to minimise the effect(s) of the event.
Although the PM is not obliged to agree to an extension of time to submit a quotation, it is a procedure incorporated into the NEC contract to allow for the fact that circumstances don't always allow things to occur in a timely manner. If the PM agrees to the extension then he should notify this to the Contractor. If he doesn't agree to the extension then I would expect the PM to state the reasons why.
Where the PM does not respond to a submitted quotation, then, following the Contractor's notification of this, the PM must reply within the period stated or the quotation will be deemed accepted. So the PM has to be given a 'second chance' to respond before deemed acceptance.