If industry generally is anything to go by, a quality manual is not an issue. You hire a consultant and for a few k he produces an ISO9000 quality manual for you.
No exception here - even easier in fact, template manuals are available to be used in a "insert name here" process. Same with the Operations Manual requirements, most Flying Order Books or similar will suffice with a few changes. Costs? Yes, that could be trickier. Much like the recent re-registration of RFs at £100 a go after years of it being free. Sadly the cost will have to be passed on to the customer one way or another, the margins in most flying training simply aren't high enough to absorb excess fees - our own PPL training has a £1/hour margin, fortunately it's a sideline we rarely do! More painful were our £4000 FTO approval fees...