I got the auto because I tow (a lot). The manual came with a dual mass flywheel which makes the engine feel smoother by reducing the irregularities of the 4-cyl engine (it's not a perfect smooth 750rpm at idle) but the face of the flywheel that the clutch makes contact with tends to heat up rapidly when feathered under load. Boat and caravan owners alike have all complained of this, replacing the entire setup with a single-mass flywheel and Exedy HD clutch.
As for the smoke, it could be several things at play here. Since it can be driven without smoke, I'm not thinking there's anything wrong with the injectors (but a bottle of good injector cleaner never hurts).
1) Dirty MAFS - quite common. It's a really delicate (and expensive) component in the air intake just outside the air filter box. Using electrical contact cleaner spray (or MAFS cleaner, it's the same stuff), spray into the small opening in the bottom while holding it over some rags to catch the residue. The stuff dries really quickly and won't affect your engine. The MAFS measures the amount and the temperature of the incoming air so that it knows how much fuel to inject.
2) Slow turbo response - unfortunately common and can be expensive. If you're lucky it's just vac hoses that are a little loose or cracked (repair cost about $20, and an hour of your time). If you're only a bit unlucky, it's the boost control solenoid (BCS) that lives on the hard pipe of the intercooler on the left hand side of the front of the engine bay (sorta close to the alternator). About $40 for a Chinese cheapy, somewhere towards $300 for a genuine Nissan one, or $175 (plus shipping) to be rid of the thing altogether and have a
Tillix valve. If luck really isn't going your way, it's a problem with the turbocharger itself. I'm (technically) on my third, but I tow a 2.5T caravan everywhere, up and down hills, through the desert regions ... it works the car hard. A genuine Honeywell Garrett 2056V will set you back around the $1500 from Brisbane, and (if memory serves) it's somewhere over double that from Nissan. Instructions for checking the turbo are below.
3) Poor quality fuel - sorta common. Australia doesn't get the best fuel in the world - it's not bad, but it's not the best. I wouldn't blame biodiesel content, because I've had a tankful of 20% (or so) and I've never had a better run with the caravan on the back. Best bet is to buy from a servo with high turnover, like a truck stop. The fuel at smaller stations tends to sit in the tanks longer, raising the chance of waxing (small crystals of wax that can block up the works).
4) Stuck EGR valve - it's been reported a few times. The EGR valve is designed to cool combustion temps so that the engine produces less NOx (greenhouse gases). It's not supposed to open at full throttle. If yours is, that will explain it - there are basically 3 choices here. Do nothing and roll coal like you have been (google that for some horror), replace the EGR valve (Nissan want your first-born for this one) or just block the EGR (1mm stainless plate on the EGR valve side of the gold EGR tube will do). Blocking it will actually return some power to the engine, but it's also illegal, so don't point it out.
Inspecting the turbocharger: basically three things to do. Two of them require you to remove the air pipe from the front of the turbocharger (the one coming from the air filter). The last requires that you remove one end of the soft hose that runs forward from the baffles (top of the motor, left hand side).
With the front hose disconnected, try wiggling the shaft of the turbo (cold engine, clean hands). It shouldn't have any sideways movement. Now try spinning it - it should turn smoothly but sluggishly. If it wobbles or feels rough to turn, chances are it's toast and the next test you're about to do will fail.
With the charge air hose disconnected from the baffle, wipe a fingertip on the inside of the hose, then examine your fingertip under a bright light. If you see sparkles in it, chances are your turbocharger's impeller is grinding on the housing or its bearings are wearing badly. If you see this, the turbo may be toast - but to be sure, check the oil on the inside of the small hose that connects to the air intake just in front of the turbocharger (this is the PCV hose). If this is clean and the charge air hose isn't, the metal flakes are coming from the turbo and you're calling Brisbane.
And you thought YOUR post was long.
Fingers crossed that it's just the EGR valve and you're happy to block it.