With the other shader that Iwas using, the one that only reflects the sky cubes(Steempipe's), I could set alpha transparency with this:

Code:

---

 
                AlphaBlendEnable = True;
		ZwriteEnable = True;
		ZEnable = True;

//  Main point is that pixelShaderConstant 'W' will control the alpha tranparency.  The XYZ will adjust some coloring.

		PixelShaderConstant[0] = {0.80,0.80,0.92,0.88}; // x, y, z, w 

---

,before "VertexShader = compile vs_1_1 WaterBump_VS();"