You probably want to get an S4 ECU over the A6 ECU, the A6 ECU is tuned more conservatively. I guess if you tune them both it might not matter. One thing you could try to do is get a 2.7 bottom end, bolt 2.8L heads on with 2.8 cams, then port an older style 2.7L intake manifold to match the heads. The newest style 2.7 isn't necessarily a better choice. You've got some options here.
VR6 swap would also be nasty.