Check your fuel filter, and check for fuel leaks... Check the clear (or if it is like most of them now, the cloudy) inlet tube from the fuel filter to the injection pump for bubbles (sign of it sucking air somewhere..... Make sure your connections to the pump are tight, and the sealing washers are in tact..
Next on the list would be to check the timing which would require some special tools... Check out here for a good description of the procedure..
http://vincewaldon.com/index.php?option=com_content&task=blogcategory&id=14&Itemid=28You got the valve clearance covered, the next would be to have the injectors tested.. This would require removing them and having someone (like a diesel repair shop) pop test them...
While you have the injectors out, if you have access to a compression gauge it couldn;t hurt to give that a check..
Is this something that happened all of a sudden, or has it been gradual?? Any chance of bad fuel? (now sure how your diesel is down under) It coudl also be possible that either your idle is set a bit too low, or you culd have a bad motor mount or two which would make it feel alot rougher...
Good luck!!