Okay, I think I can finally say that I actually understand just what the heck I am doing. I've left a little note right beside the "engine" behind it all. I'll post it here and you can have a look.
<!--c1--><div class='codetop'>CODE</div><div class='codemain'><!--ec1--> //Note on the piece of code below: each line, numbered 1, 2 and 3, are each separate "generators" of waves, each controlling the different aspects of the harmonica model. The first line controls the height, direction and speed of the wave. The second line controls the direction, speed and height of the entire surface. The third line controls the direction, height and speed of each wave. The value changed is "waveLength#" (waveLength1 is equal to 20 right now, wavelength2 is equal to 0.01, and wavelength3 is equal to 10). For example, setting the second and third line to 0.01 (minimum value) while keeping the first line as the same number would make the waves go in a single direction, without changing shape or breaking. Setting all numbers for "generators" to an equal value would create perfect hamonic waves. If you are not satisfied with the waves in this mod, please modify the the values that right now say "20", "0.01" and "10"Â
// Weathers[n].Sea.Harmonics.h1 = direction1 + ",10.0000,1.0000,0.00,0.00";
Weathers[n].Sea.Harmonics.h1 = direction1 + "," + 20 + "," + seaStrength1 + ",0," + waveSpeed;
Weathers[n].Sea.Harmonics.h2 = direction2 + "," + 0.01 + "," + seaStrength2 + ",0," + waveSpeed;
Weathers[n].Sea.Harmonics.h3 = direction3 + "," + 10 + "," + seaStrength3 + ",0," + waveSpeed;<!--c2--></div><!--ec2-->
I might even write a tutorial for the POTC modding wiki.