Seems like two seperate problems here: pump control and pump timing
Control: When you have have the pump in your hand you will see a small lever on the body of the pump below the gasket
surface and above the spring. When the pump is installed this lever is moved left and right by the control rod and its function is to turn the plunger in the pump body thereby lengthening or shortening the duration of the injection stroke, thereby giving more or less fuel.
The control Rod is the flat piece of steel
which you can see down in the pump cavity in the block. The control rod is moved by the governor in response to your movement of the throttle cable or stop cable.
When the pump is placed into the block, the tip of the small pump lever needs to drop into the notch which you see in the control rod, thereby allowing the governor to control the fuel pump
output. If you miss the notch, the pump lever lands on top of the control rod and when the pump is tightened it binds up everything....pump, rod, etc. This results in the situation which you encountered.....engine RPM
which can't be controlled.
Hopefully, nothing got bent or damaged during this episode. After installing the pump you need to be sure the control rod can float freely fore and aft. This is done by removing the large hex head plug
on the rear face of the block aft of the injection pump area. The aft end of the control rod resides there and you should be able to move it fore and aft easily.
Timing: This is a bit more of a problem........
Timing can be set with the special tool, or a degree wheel
and fuel flow pipe(Wilber tube), but probably the easiest thing to do is just what you have done.....two soft and one hard shim. I think I would go with one thin gasket
and one thick gasket, as that puts you in the middle of the adjustment range.
Failing that, scrape off all the paint
around the pump opening in the block and see if you can find any markings. Consider no markings to equal "0".