You'll be happy with your choice the first time you take it offroad.
I'd go for a GU8 if I were you (April 2012+) as they got the most significant upgrade since the CRD motor in April 2007. The STs got the TI/ST-L rear aircon (second compressor in the left rear quarter panel and roof vents for middle and rear seats), and all GU8s have traction/stability control, plus a switchable rear diff lock (as the LSD did not play well with the TC).
You'll also be buying one that is still in its 3 year warranty, which is good because if it's a keeper you can get the warranty extended another 3 years or up to 150,000km, whatever comes first. Ensure that it is a factory warranty though, and not a dealer warranty which is a waste of money.
As for what goes wrong, there's a few things, but none of them will stop the vehicle.
- intercooler header tanks can crack
- exhaust manifold can warp (CRD runs extremely hot EGTs and the manifold expands so much it stretches the studs in the head, so then it's loose, and then it warps)
- EGR pipe that runs behind the head can crack
- serpentine belt tensioner can fail (shared issue with all ZD30s from 2000 onwards)
- oil weeps on block
- TPS (throttle position sensor) can play up
- have heard of leaking injectors and relief valves
- dash top can bubble on earlier GU IV but that might have been resolved by 2010+
- rear coil hats/brackets can crack if the vehicle has been used on rough surfaces whilst heavily laden
None of them are 'common' faults, but they do occur. Ways to fix them are documented on both NissanPatrol.com.au and Patrol4x4.com but if you have warranty you are a happy camper!
Personally I'd go auto over manual, this is because the ZD30 is about power, not torque - it loves a good rev and a 5-speed box keeps you pretty busy. Auto is more fun offroad too and in low range it descends steep terrain with good control when locked in 1st. As for outright performance, average when standard, and worse if you fit 33" tyres. But a larger diameter exhaust with high flow cat really wakes it up, a chip even more so. You can also fit a more efficient intercooler, and even a taller intercooler scoop (proven to lower intake temps significantly, and by extension exhaust gas temps).
Fuel economy is a weird one with the CRD. Some people report 11.5/100km (close to what Nissan claims) and others are up around the 16-17l/100km mark - and it makes no difference whether stock or modded, snorkel or no snorkel etc. Mine averaged 15-16l... we're no closer to working that one out as the various topics on this have led nowhere.
My 2008 auto on 33" tyres had a 3" Scotts Rods exhaust, Steinbauer chip and EGR block, and it would happily pull a tonne of camper trailer up a mountain pass without raising a sweat. Zippy in traffic when unladen too. I'm not a fast driver but I never felt the need for more, and my other car is a Territory so I had a good yardstick for the CRDs performance.
If you're looking at an example that has done a bit of work while laden (either all kitted up for camping, or set up to tow a heavy van), get under and have a look at the rear coil hats - lots of weight can lead to them cracking. Superior Engineering makes a good bolt-in brace kit to head that issue off. If the car has oversize tyres, check the big barn door for cracks.
If you want to see how particular the dealership was with servicing, look under the front and check whether the steering lock stop bolts are in place. They vibrate out... my dealership noticed when this had happened and they fitted new ones.
If it hasn't been done, a second earth strap from body to chassis is a good thing to do, as the factory earthing is a bit ordinary.