I can't read your attached instructions well enough, but here is how I would put this: First, the flat part of your metering rod arm should sit parallel to the flat section of the pump lifter link. In an ideal situation, they'll be just barely touching and parallel. To adjust this, at the bottom of the float bowl, there is a link rod which can be bent to adjust the travel of the pump lifter link. I'm assuming you don't have one which was designed so that only the rear edge of the metering rod arm touches the lifter link only at the rear edge.
Once this is ok, you need to adjust the metering rod. To do so, press down on the top of the pump shaft until it won't travel any further. Often there is a small clip on the pump diaphragm rod which stops movement but some models lack this. If your rod has the slot cut in it and the lower diaphragm bonnet, it needs that little clip. When the pump shaft won't go down any further, your metering rod should hit the casting (meaning it should bottom out) at the same time. You can usually see when it bottoms out if it does so before the diaphragm rod bottoms out or press on top gently if you think it hasn't bottomed out yet when the diaphragm rod bottoms out. If you need to adjust that, carefully bend the lip on the metering rod arm.
To me it sounds like your pump lifter link needs to be raised or your metering rod is bottoming out much too early. Either one might cause what you described.
