You have two different matrices to choose from in your effect, that's matMtl and matEffect (in beta). Changing their values between passes is not possible - thus you can only change two fixed function texture-coordinates in realtime. Anyway, you can still enter the matrices directly, like you did in your last pass.

What you could try (I'm not sure if it works), is entering the matrix directly and use the vecSkill-vectors for the _m11 and _m22 entries.