I thought I should report back on progress.
The gearbox is now on its way back from Vitesse. They have been fantastic, professional, and have responded promptly to all my emails and phone calls. It was probably the more expensive option to send the gearbox back to them for repairs but they are specialists and I feel confident that they have done a good job. Unfortunately the real cause of the problem does not seem to be all that clear and I can only hope it never happens again.
To quote their report: "We have checked all gears, synchros and hubs and they are in good condition.
The issue was that the shift rods became out of sync, possibly due to gasket/ seal wear but we cannot find any other issue. We have replaced all gaskets and seals as required, including the rear oil seal which was heavily worn.
We have also welded the remote lever as discussed, and fitted a new clutch release bearing and fork assembly.
We have also filled the gearbox with fresh Mazda oil."
The welding of their remote lever (internal parts) was just a security measure to bring it up to their current manufacturing standard. Not really necessary.
I had already decided to replace the clutch whilst the gearbox was out and they gave me an excellent deal on the required components that had been in a car but with less than 10 miles on them (one of their auto conversions?).
Definitely recommended as a company to deal with.