I'll ignore whether this is such a good idea -- you obviously want to try. It's not like you're messing with the shear line of a Hinckley B40 (and it will be fun to listen to dock
walker try to figure out what it is)
I think your biggest challenge is that hull
is pretty lightly built. The moment you cut off the deck
(and flange) the topsides will spring into some interesting irregular wavy shape that won't resemble the deck
. You'll never get it back in line. So I think you need to first build a new flange below where you will cut to keep everything in line while you put in your shim. This could be temporary (inside or outside) screwed every few inches or be permanently glassed on the inside (a bow to stern shelf?). Even with this, rig a half dozen 2x4" across the width of the hull just below the cut.
To disguise your handiwork and cut down on the fairing, you might consider applying a chunky (say 2" high) rub rail (painted wood would be fine) on one or both of the seams. This will make any funny
bend in the topsides hard to see and might actually disguise some of the topside's vertical height. You could then pick a contrasting color for a "belly band" look. Not my favorite look but might be quite handsome here.