i wouldnt use any polyester putty on it for the simple fact that bondo and similar auto poly putties love to absorb water and swell. Id get some plumbers 2 part epoxy and use that in the troublesome areas. the epoxy wont absorb water and is also stronger than poly putty. I believe you are still going to make this RC.
A few layers of an epoxy Gelcote would work too, they come in a paintable form and could be used in a similar fashoin as Mr Surfacer on a project in this size.