Hi Dave,
I have done this, (Not on something as quite as big as the QE), and this worked for me.
Join the Hull halves together, including any internal bulkheads stiffening), I did try to apply glue to the upper sections of the bulkheads only (worked on most of them), and fit the main deck, basically get a nice rigid structure.
Mark just below the waterline all round with masking tape.
Then carefully and slowly, with a razor saw cut just below the masking tape. Once cut all round the lower hull should just come away, trim the bulkhead flush, I used side cutters to remove the lower section of the offending bulkheads.
Sand the lower hull to the exact waterline your require. it as advisable to keep checking the you don't sand in a list.
Hope that helps.
Cheers
Si