It is simple to check for proper timing.
Just pull the number 1 injector and the valve cover. Put a wrench on the crank or use a baring tool and turn the motor over. Using a piece of plastic tubing, like a nozzle from a can of carb cleaner, stick it down the injector hole. Watch the intake valve to see when it is closing. 180 degrees of crank rotation from the valve closing will bring it up on TDC. Use the plastic tube to varify the piston is up.
Note: using the plastic tube will insure a "no heart failure" condition in ones body if you drop the tube into the cylinder. The engine will just "eat" it when you start it.
After making sure it is on TDC, check to see if the timing plunger will lock into the timing hole. You may need to "rock" the engine a little to find the hole. If you cannot find the hole, turn the engine 360 degrees more and see if it will lock in. If it does, the pump grear is 180 degrees out.
I hope this is not the case for you. But it would be good to know. That way, you can rule out timing and look deeper into the pump.
Dave