The specifications for commercial diesel fuel are in the public domain. As far as I know, the key tests to perform with respect to the injection pump and its' durability are fuel lubricity tests (Dieseldude and 4JGtootsie - please correct me if I am wrong).
The standard lubricity tests involve either a sliding ball or a reciprocating rig test. The DOE (Department of Energy) lab in Fort Bonifacio has both types of testing equipment. They charge a standard fee (about Php 5000 each) to do the tests and the results are a matter of public record.
Again, as far as I know, the oil companies like Shell and Petron are required to have these tests performed on their fuels regularly. The records should be available at the DOE. The oil companies themselves should be able to produce the results of these tests, (as well as those of an independant third party lab) on demand.
If these tests reveal that the fuel supplied by them (the oil companies) meets the standard, then it is likely that there may be contamination or adulteration at the point of sale (the gas station). The next step would be to perform similar tests on the station's fuel to confirm.
If however the station's fuel was found to conform to specification, then the only possible conclusion would be that there is something terribly wrong with Toyota's design.
Should Toyota subsequently claim that the local diesel fuel does not meet their engine's requirements then the answer to that assertion is simple - that knowing this they should NOT have SOLD their engine locally.
Having done so with the full knowledge of the fuel problem is a matter of bad faith.
As to the issue of filtration, I am of more than one mind.
If the problem is fuel lubricity, then NO amount of filtration will provide for or increase that property, the fuel itself must be blended and formulated with the proper amount of lubricity.
The funny thing is that creating excess lubricity - and this should really be a sore point - is NOT expensive as increasing the fuel's lubricity is usually done by adding the proper lubricant in parts per thousand (fractions of a centavo per liter of diesel).
On the other hand, if the problem turns out to be contamination, then there are real benefit's to be gained by proper filtration.
The main difficulty would be that a finer filter would clog or choke sooner and would have to be replaced more regularly.
Furthermore, placing another filter in series with the existing set would lower the supply pressure to the injection pump and choke the fuel supply.
You would be surprised how much horsepower you would lose after you put in the extra filter.