Thanks for the replies everyone. The gearbox mount has been changed too. The problem was not present before with my old mounts. Yes, the engine is sitting higher so a general change in alignment could be an issue. There is a mild drumming sensation too when driving at 50 -60 mph say.
Don't whether I should defend my indy or not but he offered to replace the rear diff mounts, diff seals, ABS sensor seal and reseal the back plate for £300 plus parts. The seals are only being done because the diff's coming out, not because they are leaking excessively. Please let me know if this is too much!