I've gone the treatment root, recycled the fuel and replaced fuel filters in the past. I don't recommend that approach. The filters are more expensive than the fuel you are trying to save. Pump the tank dry, and if you can remove the inspection cover (some tanks don't have this), reach in and clean the junk out of the bottom of the tank. I learned this weekend that Mark Rotsky (Nemesis) uses an oil change vacuum pump to reach in and suck out as much stuff as he can. He does this every year.
Once clean fuel is added, do add the diesel fuel treatment and water absorber to prevent growth.
The fuel injectors can be pop tested by a diesel mechanic to check for proper spray pattern. A clogged injector will exhibit smoky exhaust and rough idle. I had the diesel mechanic at
Oldport Marine in Newport, RI pop test, replace tips and shim my injectors for $80. It fixed a rough idle problem.