The critical and easily damaged piece of the injection pump removal is the shim pack under the pump on the mounting base. That shim set determines the timing of the injection. On removal, be very careful not to crimp or bend or crease any of the shims. Usually will have more than one.. when going back, the surfaces need to be surgically clean.. no grit, no lint, nothing A very thin smear of high temp silicone applied and torqued down before it starts to set can be used to keep the shims from leaking.. The other critical part is the governor arm connection with the fuel rack pin on the side of the pump. You can see this once you remove the little cover plate on the side of the housing just below the pump. Take a picture before you take apart so you can see exactly how to get it back together.
While you have the big gear cover off, it would be good to replace the oil lip seal where the crankshaft comes through the cover I think it is a "25408" metric seal .. you can buy one at a bearing supply place or many auto supply places .. the number means it has a 25mm hole internal diameter, a seal external diameter of 40mm, and is 8 mm thick .. The Yanmar part number is 121450-01801.
EDIT.. don't "adjust" the fuel balancing screws on the side of the injection pump, unless you plan on taking it in to an injector shop for setting.
