I'm not sure the 500ppm diesel (referring to the sulphur content) would have caused that problem, but given the pressures inside the common rail it can't be discounted completely.
The 2007 D40 that I know of uses a variable vane turbo, there's no wastegate. The vacuum lines are used to control the vanes, which adjust the flow of the exhaust gas over the turbine that drives the impeller that creates boost. Wastegate turbos were used on the D22 series, but Nissan have shipped different spec cars to different parts of the world so there's no telling, really, without a visual inspection of the turbocharger. I'm not sure with any certainty that your problem lies in the turbo or the injectors though.
To be thorough, you might consider putting a bottle of a good injector cleaner through. I just ran a bottle of Liqui Moly Injector Cleaner through mine and it did fixed the slight surge in cold idle that I was noticing.
I'd also closely check the EGR, hoses and intercooler. The EGR is a two-way street - it will allow exhaust gas in, and will let boost pressure out. Blocking it by replacing the gasket with a blanking plate is the best way to deal with it, and make sure to use gasket sealer to ensure a good seal (on both sides of the plate). The hosing between the turbocharger and the intake manifold could have leaks - look for what appears to be an oil leak. I've just found my second one - the hose that joins to the intake manifold was leaking, and now the one on my baffles is leaking. I'm about to replace ALL of my intercooler hosing with silicone hose.
I'd leave things like injector replacement for when you've finished trying the less expensive things and haven't solved the problem. Injectors can be tested, but even that's not cheap.
I doubt an ECU program fault, but a fuel mapping fault is possible: just reset the ECU and it will go back to factory settings. It's easy to do - take the negative battery lead off, go press the brake pedal, then put the battery lead back on. Make sure your radio PIN is handy, and write down the trip meter values (if you use those for recording economy) first, because you lose this info.
Water can still get past the filter. It's not a perfect water trap, and some of the guys here have been putting separate water traps in. Water can damage the injectors - it becomes quite a powerful cutter at 30,000psi. Let's hope it's not that.