Thanks for the feedback and questions, hopefully the following makes sense.
I agree its great kit and I'm not complaining.
Here's a photo showing our layout, it was as per the plans with the piece of aluminium angle fitted on top of the spinner with a washer to allow for future engine drop due to mounts settling.
And here is our new repair done this weekend, we built up the inner surface with flox and epoxy then sanded the fiberglass back on the inside.
Note the pink area is the original fiberglass height and the white area is the extra flox mix we added and shaped to match the original contour.
I am not sure if this reduction in the intake will affect the flow of air for the engine, any thoughts on this?
And finally here is a photo of the raised area with rubber inserted to check, looking good now.
The Vans plans call for using a flox and epoxy mixture to fix the sides so we used the same technique and mix to raise the cowl scoops, I believe using fiberglass is not good as the edges of the glass may show through the paint (but I've not seen this problem).