Im no expert on twin deisels, but Id check the linkages are opening both pumps equally as a preliminary check. With motorbike twins, to synch the carbs, one cylinder is disabled by shorting the plug lead, the other carb is set up to run the engine at a known rpm. Then the other cylinder is adjusted the same way. Then with both cylinders operating, the idle speed can be adjusted.
The same approach should work on a diesel twin, read pumps instead of carburettors.....
If injectors or pumps are suspected faulty, try swapping them side to side., if the weak cylinder follows, you have isolated the problem. Just do one thing at a time, else confusion quickly sets in.
Thats what I would do......