Had a little thought the other day about using standalone engine management (megasquirt because its cheap, diy and I'm familiar with it).  And leaving the ecu hooked up to control instruments, ancilleries etc (parallel install).  I suppose a cable throttle would need fitting and traction control would be lost.

Anyway I guess the me7.1 would need a few thing changed so that it monitors everything but complains about nothing.  Just quietly thinks its in control.  No CEL, no limp modes.  Would this be particularly hard to do?

You're right but...Well it would be a lot easier to work with.  Make adjustments while engine running with maps described in plain english instead of crazy acronyms.  Plus I have one gathering dust that will probably end up on the lawnmower if not this!

Megasquirt will never get you even close to what ME7 is capable of.

you can run to the limits of knock, for example.

This was done back in 2005-2006 on a B5 A4 1.8t; he DID have to piggy back onto the system if I remember correctly, but if you dig on the MS3EFI boards you might find some useful information there.