You now know that was a wrong move to have him put the box back in, but you were not to know, to be honest he doesn't sound the most helpful of chaps, most good indies will try and mitigate the costs for their customers including sourcing used major units, failing to save you money means you might as well be using the main dealer.
Just remember if you source a gearbox which proves to be faulty, it's your risk all the labour involved continually removing and refitting.
If it were me i would be inclined to find another mechanic in your area, possibly by recommendation via a VAG forum or ask around friends and workmates for a good place, a good make specialist indy should have ready contacts for such used parts and have a good working relationship with them, this is the case with my MB indy who if some seriously expensive part fails can have another one there from a trusted used parts source in a couple of days.
One thing, if you become disillusioned and decide to part with the car, do not be too keen to let this mechanic have it for a song (i've seen events like this unfold before), if it eventually comes to you selling it still faulty, advertise it with a truthful description on ebay.
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