Just to clarify...
When I was recording the pre and post mdrt clips, I wanted to try to be scientific about the whole thing so I recorded the direct guitar signal with my sony mini-disk recorder and then played that back into the input of the mp1. This was the source of that noise (was quite surprised how much it introduced). I'm sure the levels and impedance and whatever were all wrong, plus there may have been unshielded portions of the setup as I had all kinds of adapters in the line. As soon as I went back to guitar straight into mp1 the noise was gone. Having said that, on my highest gain patch, I do use the gate on my g-major 2.
In hindsight, I should have set up some custom patches with flat eq. Pre mdrt I had my treble and presence levels pretty high. Even the bass was actually a lot higher pre-mdrt than I have it now post mdrt. Post mdrt my eq is quite flat. It was like having a new amp and I just went back and started from scratch.
Also, the recording setup that I was using is pretty cheap and nasty. I also had to bring down the recording level on the distorted post mdrt track significantly as it went off the scale. There is a huge increase in output.
The transformer swap is pretty straight forward and completely reversible, so I would recommend just giving it a go.