You probably had it closer to right the first time without the washers. After replacing the busings, they may be slightly different spacings than the old ones. That is what the washers are for, to make up any differences. Sometimes you need to add here and remove there kind of thing. You can have extra washers when finished and it is ok, as long as no pulling or pushing was done when tightening the parts together. Sometimes you might even have to go buy a few extra washers.
I dont have the written assembly guide. I probably could'nt read it anyway. But I allways start at the first bushing and the arm with the cotter pin. I make those just right and press the big bushing to fit proper, then I "adjust" the rest of the bushings with washers to meet those first bushings settings. Reason being, the eccentric bearing arm and the arm with the cotter are both connected the superstructure mechanically. That makes that first big bushing's spacing very important. The rest are simply attached to the frame on one end and the chaffer and shoe rails on the other which makes them easier to adjust since the rails can be shifted and centered in the machine, and the frame end has washers as well.
Hope that made sense.