Time is always allowed to pay for parking once parked, or nobody could ever park legally !
As this is Havering, it's a total no-brainer now to take them all the way to London Tribunals as the penalty remains the same and there are no additional costs whatsoever. You took rather a time to get a permit but the reason was their website as far as I can deduce from your narrative.
Can you post your informal reps, please. In order to get them to London Tribunals, you first have to submit formal reps and get them rejected. Make them do some work as they are a disgusting council refusing informal reps and not re-offering the discount. Disgraceful, frankly.