Well, a bit of a follow up.
The gearbox investigation proved inconclusive (or so I was told), but as a "gesture of goodwill", I now have a new gearbox in my car, £50 off the clutch/flywheel work and I'm out motoring again!
All sorted in the end then, but this experience has left me completely untrusting of these big chain garages like Mr. Clutch, Kwik Fit, etc. I'll be taking the Coupe down to my local mechanic from now on, rest assured!