Best tool would be a hot wire cutter--no mess--but that might be a spendy answer for just one dio. Fine (or omnidirectional) blade in a coping saw frame will work. But, I've found a simple hacksaw blade to be near as good.
It is well worth the effort to make a good-enough template of the waterline out of cardboard or the like. This will let you plan where the ship will set in its "sea." (Do not forget to allow for the overhang of yards and of the bowsprit in this planning.)
Now, this brings us to the set of the sails. If memory serves (and it may serve me poorly) the Revell Connie is set up with the yards on a starboard tack beam reach. That would make the wind direction 45ยบ to the center-line of the ship from right rear to left front. The ocean swells will run generally perpendicular to that line. It's worth sketching those line on the foam, just to see if that angle does not conflict with the layout.
Now, we will want to cipher on how deep the swells and how far apart. Let's say you wanted the swells to be 3/4" deep/tall, that's 6' at 1/96 (1/8'=1'-0") scale. That's a 5 on Beaufort Scale, a Fresh breeze of 17-21 knots. This is going to be about the upper limit for setting stun's'ls. By dint of some esoteric formulas (all readily available via google) the swells would be from 45 to 90 feet apart--cal that 6 to 10 inches apart in the foam.
Which might just be worth laying out on the foam. From Beaufort, we know that the swell tops will be forming white-caps; this means there will be wind ripples in the troughs between the waves.
Sailing vessels do not leave a great deal of wake (comes from only going about half the wind speed) , but, there will be some.
The rest is fitting the hull to the cutout, and the carving the waveforms.