Mine is also S3 and at just under 2yrs has done 13k miles. From day 1 there was noise changing up/down in 1st and 2nd and in both these gears with clutch depressed and coasting to a stop a lot more "rotating" noise. A lot more of this is discussed in the following thread:

http://www.talkmorgan.com/ubbthreads.php/topics/33510/transmission_noise_aero_8_seri#Post33510

1st and reverse chatter at low speeds appears to be acceptable in the Morgan Aero8, but as mine is now chattering in Reverse, 1st 2nd 3rd 4th and the fault is diagnosed as the dual mass flywheel frown2, the poor car returns to Malvern in 2 weeks time for a replacement. smile
As far as I know this is only the 2nd time in the +/-600 4.4l/gearbox configs that this has happened.
When 'motoring' the g/box is generally quiet, only at low speeds can it be heard due to the lack of insulation as previously mentioned.
I also agree with the comment that the clutch is either 'on' or 'off' and it does have a long travel but I am used to this and have no problems with it.
I would also recommend contacting cerealsurfer as his garage in High Wycombe were instrumental in my diagnosis notworthy

I shall be interested to hear what you find out - at least it is not fatal (like a 20amp fuse shocked2)and I shall enjoy driving the Aero until it is trailored away pale