I doubt that you actually want separate ECU controlling the TB and the fueling, I have trouble believing that's the sensible (or easy) solution.
If you can't figure out how to make the Megasquirt control a DBW throttle
*, maybe go Haltech to control the engine (like MCM did with their EZ30, which is probably where you got this idea at all), and a standalone DCCD controller like
MapDCCD.
*-I'm sure a MS can do DBW just fine.