If the linkage is installed correctly, then the pump is likely not assembled correctly.
It's been awhile since I had one of these apart, and I'm not sure I've ever had the exact one that you have apart, but they're all basically the same.
You probably either have the plungers 180 out in the pinions or you have the pinions at the opposite side of their travel. Some pinions only go so far; some don't have stops.
How far did you disassemble the pump? If completely, I'd guess the plungers were reversed. The pinion holds the plunger in a certain position relative to the bushing so that an amount of
fuel specific to the governor position is injected. If I remember correctly, if the plungers are reversed they inject full
fuel all the time, irrespective of the rack position.
If you didn't completely disassemble the pump, and if the pinions have stops, you may be able to just remove the pump, note the rack's position at full fuel and no fuel and reinstall it with the pinions turned to the opposite position.
Obviously these are just generic suggestions that may not be specific to any idiosyncrasies of your pump, but they might help steer you to a solution...or perhaps an injection pump guy with experience with your particular pump will chime in.