I've been working out all day how to get my custom water texture working, and I finally ran across this. Retro Affect has a script that generates sprite sheets automatically, and with a little modification, it can work for the mcpatcher custom animations.
First, you have to be using photoshop.
Ok, go to the site and download the script. Unzip it and open up RA Animation Exporter v1.2.jsx in you favorite text editor. The first two lines are easy, located at the top. Just scroll down until you see
var dehaloImage = 1;
var sheetGrid = 1;
and change both 1s to 0s.
Next do a search for "Organize the frames". Above it you will find