Much sympathy for you also Bob.
Personally, I think it is a massive coincidence that your car returns from having some major work done (I would certainly call 'gearbox out' major work) only for a totally unrelated fault to be present. This HAS to be related to the work done, but there still remains a remote chance that it IS coincidence.
It is probable that the MVT carrying out the work has damaged a sensor, trapped a cable/wire, not reconnected a plug etc etc etc, who knows? I have heard of lesser quality marques frying the ECU due to the main engine earth not being reconnected properly causing the engine to find another earth through the ECU! I'm not saying this IS the problem, it could be anything but highlights how these things happen.
I think the garage taking the 'swapping parts till problem solved' approach just highlights the lack of their expertise at your expense.
This approach can be tolerated to a certain extent if you are happy with the standard of workmanship and professionalism in respect of how they treat you and your car.
I certainly tolerate this approach if a garage :-
1. Handles me with kid gloves, like I am their most valued customer
2. Keeps the costs competitive
3. Are open and honest about their level of expertise
4. Take great care over my car whilst in their 'custody'.
5. Go to great efforts to resolve any resultant problems
However, there is a limit to the tolerance that a customer such as yourself can reasonably be expected to be put to. Personally I would have been 'creating' about seven weeks ago!
I took my S3 to JBS and watched the MVT change my clutch, TIP, adjustable rear tie bars in just over 4 hours! Including a laser alignment! I drove home a happy customer with no resultant faults whatsoever.
You probably still want to maintain a relationship with the garage after this saga is finally put to bed but I would be pushing for a negotiated settlement that YOU are happy with, not the garage. You are NOT the person at fault here in any way so 'customer satisfaction' is the watchword, don't take the usual easy and well trodden British route of bending over and being shafted without so much as a whimper.
I would suggest that some of the parts replaced did not need replacing and once the new ECU is installed I would be asking for the old parts to be replaced (with you supervising) to keep the cost down and prove that they were not the cause of the fault...
As suggested, a cool, confident, business like and documented approach to this will certainly have the best chance of resolving the situation in a way that may sweeten the whole sorry tale...