I made an adapter to mount a throttle position sensor to the side of the dbw throttle body. This provides a signal for megasquirt and does not mess with the safety and reliability of the vw system. There are tons of Mk4 jetta/golfs in the wrecking yards so these parts are very easy to come by and there are many different throttle bodies that will work with these ecus, even one from a dodge 5.7 hemi!
I know from my experience building the twin engine jetta vr6 w8, that multiple ecu's will read a single throttle pedal when wired in parallel. This means there are many new possibilities for crazy intake manifold designs using multiple throttle bodies where a mechanical linkage between them is not possible or practical.