Not sure I can help you but have you tried the ECU reset to see if that helps clear the EML and restore normal operations? Here's how; http://www.350z-uk.com/topic/53148-how-to-ecu-accelerator-pedal-throttle-valve-resets/
That garage doesn't sound great tbh if they cannot even set up their own equipment correctly.
Are there any better garages nearby you could use? like are you near any of the more recognized Zed specialists from on here? eg: Horsham Developments, CS, Abbey Motorsports, TDI etc.
Free bump anyway and hopefully some more replies will follow to help you out.