Hi John,
Wow quick progress! 🙂
I had the same concern with the gearbox and it's proximity to the tunnel ... I contacted Lee at Caterham about it and he said it's normal that they're very close...but not touching. My gearbox touches the heat insulation on one side, but only just and isn't (as far as I can see) touching the metal. If yours is, I'd raise it with Caterham. Particularly before drilling any slots in the mount. Mine is an SV by the way....I don't know if the tunnel is a different size for S3 cars. Is yours an SV?
Thanks,
J.