Hi Andrew,
You have a non-standard ECU map, and presumably the running map was tailored to your specific engine.
I guess it could be that the map is now not suitable for the new build!
I'd also echo Rab's concerns about your workshop choice should they be struggling to troubleshoot this type of issue, but that doesn't help you really.
I'd expect the organisation to have the ability to inspect the performace from the various sensor outputs using scopes or data-logging equipment, and be able to understand if there is an issue with air or fuel delivery, or if the new turbo isn't working as it should because it's faulty.
If there are no fault codes being logged that is a good sign there isn't an installation issue.
Presumably you had been advised by this workshop that the turbo failure had not caused any additional engine issues, but did they actually advise what was wrong with the original turbo?
My reason for asking is this:
Your description of the fault isn't something that would usually be attributed to a turbocharger failure.
The whistling noise indicates the compressor is providing boost, but that boost pressure is escaping to atmosphere.
As the compressor side of the turbo is driven by a common shaft, then a full on failure would seem unlikely.
That then leads to the fault being the boost pipework (or intercooler) and not the turbocharger itself.
Of course, your turbocharger might have been about to disintigrate and was caught just before it caused catastrophic damage.
I should make sure the workshop understand you have a non-standard ECU map, and I trust the map you are running is a re-write of your original map and not something you've downloaded, as there are different ECU types, and each is written slightly differently depending on the type fitted to your car.
You may find that the car drives exactly as it did prior to you problem, and this is just a consequence of your re-map.
Sorry this isn't going as smoothly as it should, and hopefully there'll be a positive outcome for you soon.
Cheers
Jeff