First, this part:

My.skill1=5;// activation dsic
My.skill2= 2; //directions
My.skill3=2; //wave speed
My.skill4= 3; //skwel value
My.skill5=20; //wave size
my.skill6= 2; //crests_per_unit
my.material=mat_riverwater;

should not be in the loop. The material only needs to be assigned once, before you go into the loop, and the other values as well. You can adjust the size of the waves in the shader by changing the following values. I think if you want to use the skills to affect the values, you will have to change the shader to use them. Right now it seems they are hardcoded. Change the following line to affect the wave size:

// scale - change according to model scaleing
VertexShaderConstant[14]={2.0f, 2.0f, 0.0f, 0.0f};
VertexShaderConstant[15]={3.0f, 3.0f, 0.0f, 0.0f};
VertexShaderConstant[16]={4.0f, 4.0f, 0.0f, 0.0f};

You only need to change x and y. The smaller the number, the larger the waves.