Just do it with a shader.
Do at least the first 2 chapters of the shader tutorials first: http://www.conitec.net/shaders/
Understand a few basics like the texture coordinates (0..1, independent of your actual texture size), that a vertex shader is executed for each of a model's vertex and the pixel shader for each pixel of the model drawn to the screen (independent of the model's texture resolution).

Then you will come to the conclusion (by trial and error with an AUTORELOAD flag on the material) that you need to use 2 textures, 2 tex2D commands, one with shifted texture coordinates, one unshifted, where the latter's alpha channel determines the transparency and the former its texture.