Surging and rough idle are very commonly caused by air leaks
on the low-pressure side of the fuel
system. These leaks
are caused by aging fuel
lines/ poor connects, and are exacerbated by increased pressure from bad/ dirty fuel that causes restrictions in the filters, the lines, or even the pick-up tube in your tank. Visual inspection
of the filters will not reveal this problem.
Before you start pulling injectors or embarking on other expensive/ invasive diagnostic adventures, you should eliminate the possibility of air leaks by bypassing your tank, your old fuel, and your Racors. Get yourself a plastic, three to five gallon fuel tank
from an outboard engine
, fill it with clean, new diesel
, and connect its hose to your secondary filter (the one on your engine). If you leave the priming bulb in the hose it will make it easy to bleed the system.
The shop guys call this a 'pony tank'.
If this doesn't solve the problem, you can move on to more complicated procedures.
Here is a good thread about how much time and money
could be spent overlooking the simple solutions Yanmar Problems