I'm sure if you contact a good tuner on this forum they would be able to sort out all the engine management issues. When I first put my Audi conversion together I liked the power it was putting out (PD130 AWX), but once VWMikel had it tuned it was a completely different beast. That being said, the PD motors like yours (and mine) do need a tune to be able to compensate for the larger components you have. Idle regulation can usually compensate, fuel maps will need to be tweaked, and everything with the charge air pressure (turbo's) will need to be re-written. Especially due to the electronic VNT mechanism. It has a map that it wants the specified manifold absolute pressure to follow at the specific position of that Vane, when the actual pressures aren't following that map it will kick the engine into limp mode and cut the fuel back drastically.
I'd say the expensive part is over, I wouldn't think a tune would cost too much, there are 2 ECM's to deal with though so it may be more than standard. I wouldn't think it would cause too much of an issue with a tuner though as one ECM is the master controlling one bank of the engine and the other slave controlling the other.
Since you'll have the only renditions of this type for now
, you'll have to do some data logging, some communications between the tuner, and a couple versions of the tune, but any of our tuners do this for no additional charge usually.
Sounds like you are getting close to being complete with this project, I'd like to see some videos of it going when you get finished (with a tune of course).
Good work
Jon