Paul as someone that actually owned one of these for a number of years, not just test drove one I can tell you that the manual is fine. The clutch issues arrise when people forget that they are driving a manual and towing heavy loads. The power delivery on these engines is not really suited to a manual if you are doing lots of stop start towing. I used to use low range in mine a bit on steep hills etc to take the load of the clutch and it was fine.
I also had a 40mm Dobinson lift in mine and still prefer the way that drove to the D4 that I replaced it with. To a certain extent the 17" rims that I had on mine would have contributed to the ride but it was just so bloody smooth compared to the bags on my D4.
Finally with regards to TR, there is much to be gained if you are doing a significant amount of offroad work but based on what you have been saying it will still be able to go most places as the traction control part is still in there. The upshot of the S is that it is very easy to replace the stereo with an aftermarket unit as there are none of the issues with the dash on the flasher versions either. I had a pioneer double DIN unit in mine with reverse camera, DAB+, DVD and could run iPhone Apps as well as a bunch of other stuff that I never bothered with. I will never be able to get all that in my D4 without interface issues.
I sold mine for $25k but it only had 134,000km on it and was a very good condition with a lot of new/replacement bits on it.
Cheers
Paul

