Well done re re-build, I have my fingers crossed that I'll get it up and running in the next 6 months or so
although it's probably wishful thinking...
In terms of those decisions, any advice of what works will be greatly appreciated! Given it's mid-engined and I don't wish to run boost pipes all the way to the intercooler bracket in the front I was planning on using a chargecooler and piping to a second front radiator- unless there is sufficient airflow in the back to cool sufficiently (modify the bodywork to increase airflow)? For air induction I was planning on keeping my current conical K&N air fliter (unless I've misunderstood your question...)
The wiring is going to be complicated - I currently have a recoded VAG ECU but I've just discovered the new ECU from my turbo donor car is different. If I go the recode VAG route I imagine it would be more sensible to keep the ECU that is paired to the engine and swap all the connections on the car side loom to the new ECU socket, then recode the ECU. I don't know anything about aftermarket ECUs - I imagine you get more control over the software but I don't know how easy it would be to wire up.