forget about the timing marks they don't mean anything for setting up the injection pump.
You are correct the shims only change it a few degrees, and the shims only need to be changed if you did work to the block, like mill it, not anything to do with the injection pump, even with a pump rebuild it doesn't change the factory shims.
Do not use any sealer on the shims as the sealer adds thickness and will throw it off even more.
The only way to change timing is to pull the front gear case cover off and change the gears, have you done that?
If you haven't pulled the gear case then it can't be out of time, it also wouldn't fire on just 2 cylinders if it was out of time.
Pull the injection lines off of the injection pump set the throttle to high and crank, you should be getting fountains out of all five delivery valves to the same height, if your not you have an injection pump problem.
Have you adjusted the valves?
Have you done a compression test?
That's a direct injected engine, it will start and run without glow plug.
The injectors are stanadyne pencil injectors, very easy to bleed.