Yes you can eliminate the transmission control. Essentially what they do is go into the computer and select manual transmission. You can then use a 904 or 727 or even a later 4 speed automatic.
And as far as limiting the VVT is concerned, for the DIY Megasquirt and similar crowd, it's worth it...
MS3 allows for VVT. Although I don't know of anyone who has actually used the output on MS3 to make it actually work. You'd be at the bleeding edge so to speak.