Montegue, Looking at it, it seems to me that it has been, I'm reluctant to say engineered, around a bought in rubber mount. I have a 2010 duratec with the MT-75 Ford gearbox and that mount is tucked up tightly into the transmission tunnel. The contraption that Morgan fitted to the Mazda boxed version seems almost ludicrous, something from the age of steam! If I try to give them any credit, hard I know, but again the unsuitability of the Mazda box transmission case having that mounting web hanging down.... was it to try and protect that?
Anyway Montegue, You have made a beautiful job of trimming the lower bell housing web could this web be made more acceptable too? On my car when I first got it I was shocked at just how close the gearbox case was in relation to the chassis cross member, at its closest point only about 5mm. I thought something must be wrong with my car, chassis deformation, collapsed mounts etc. But no, all was correct and I can tell you under all driving conditions there has been no contact at all between the two! This would indicate only micro movements are occurring here,I think I would remove the complete mount, obviously support the gearbox whilst doing so, and aim to modify the depth of the mount by drilling new mounting holes so it sits higher in the chassis and look to separate the mount from the box using high impact rubber sheet of 10-12mm. If I push and pull at my rear mount nothing moves at all so it is only acting as a vibration separator with the MT-75 box fitted so I can't see any issue in doing similar in the case of the Mazda box! Vitesse who supply after market Mazda boxes for Morgans don't seem to have all these fitting issues with their casings, might be worth having a chat to them as I'm sure they must have answers re sorting an original fitment.