Don’t despair, my car had a similar tolerance build-up in the chassis, and the Mazda box is a tight clearance. First thing to try is to make yourself a wedge out of 70x70mm planed softwood, it needs to be 250mm long. Loosen the engine and all gearbox mounts. Place the wedge down the LH side of the box with the thin end between the box and lower chassis rail. Doing so will not harm the powdercoat. There should be good clearance to do this in front of the gearshift aperture. Watch you don’t damage the plastic switch housing on the side of the box while working in the area. Use the wedge as a lever, and you can drive it downwards to max the gap between the chassis lower longitudinal and the gearbox case. Once you have optimised the clearance in the contact area forward of the wedge, torque up all of the mounts starting with the box first. Don’t expect much of a clearance but you should gain a few mm and all should be fine once you are on the road. There is a further mod I can vouch for if it is needed which will give added clearance and so far has been good for the first 11,000 miles in my S3. If you think you might need this after the end of this month, PM me beforehand with your email and we can exchange contact details.