take separator off and take it apart. See if there is anything in the fittings. If there is, clean them.
ideally you'd do a fuel flow test using a nurse tank of some sort to keep the engine running while you test the rest of the system. Easy to do but for some reason many don't think about it, sometimes including seasoned technicians. They'd rather chase all sorts of "problems" that don't exist, injection pumps, injectors, primer pumps, tanks, etc. Couple hours later, they clean the separator, problem solved.
You would be surprised how many 30+ year techs I've seen that would get an engine in (diesel), with a noise or low power issue and immediately pull the pump off/out and send it off. $1000-$1500 later (plus labor), still same problem. People seem to think that because it's a diesel and its not running right, it's automatically got the most expensive problem possible. In my experience, it's almost always something simple, thus I tend to start with simple stuff FIRST, most of the time the problem is solved within an hour. About twice a year, have to replace a pump, about once every 3 years on average an injector or two. Honestly rare, and most of the time it's water or gasoline related.