Welcome to the forum.
As they've said. The V6 diesel has had a couple of minor issues - nothing with the major part of the engine - early models had turbocharger hose weaknesses and recently some EGR valve failures have come to light. The V6 diesel ONLY comes in auto and the programming is not ideal for steep descents but otherwise it pulls better than a 13 year old schoolboy.
The 4cyl YD25 diesels come in 3 different varieties: the 140kW, 126KW (both in the D40) and the 96kW in the D22 - as Ian says, add a chip and the D22 has similar power to the D40, but the D22 has a shorter dual cab (less rear leg room, difficult to put a baby seat).
All of them tow 3T. I don't understand why the V6 diesel can't pull 3.5T - the bloody Pathfinder can.
They're all quite capable off-road. The D22s are slightly narrower and have a shorter wheelbase which makes the D40 better for towing. The D40s also make better cruisers because their seats are better - nothing you can't fix with a spanner, just ask Sparra.
There are some other technical differences (like ABS application & usage, 4WD engagement etc) but they're all sturdy, proven, reliable vehicles. You'll get lemons out there, for sure - but for the number of Navaras on the road, the number of complaints are relatively small.
Oh, as for the 3L grenading - that was more the 4cyl 3L that was used in the Patrol and the newer (fixed) version used in the Navaras. You'd only get one second hand now.