I did check a number of the fuses, but I will go back and check them all, verifying using an ohm meter.
The timing mark on the flywheel and not corresponding to where the crank pulley was supposed to be has me perplexed.
I bought this 1996 D1 300TDi two years ago from a friend that imported it from Japan in 2013 I believe. He changed the timing belt and upgraded to the later 300TiDi belt alignment bits. The reason I am wanting to change the injection pump is due to a really bad tanks of fuel, full of water and dirt, that overwhelmed the fuel filter and caused the engine to stumble when driven at 50 mph and above. I've already had the injectors rebuilt with new nozzles, which made a huge improvement but there is still a stumble, hence changing the injector pump.
I should have read James Martin's comment more closely concerning 'it takes 2 turns of the crank to get the pump pulley to turn once'. I should have done this and checked where valves #1 and #2 where and where the slot in the pump pulley was. When things were not lining up I should have stopped and had a beer and thought things through more closely.
Thanks for all the help so far.