Depends on what tools do you have? I dont know if Tugboat will agree with me, but i would use a cordless drill with a scap bit(or with a knife). and just make several pass along the lenght, then just break the peices out. Might not be the best opinion but only one i can think of with common tools.
I woulda filled the inside with something to keep it from expanding in there NativeCap's idea sounds reasonable. Then follow up with sandpaper to smooth it out.
Above is the cleaned out hull section that has been filled in so far. I was wondering, Is the stringer really right on the waterline? That is where it measured approximately 1 inch below the subdeck. Does it look close? Cheers