Thomas, the timing would only effect running on gas, not diesel. Since the MD runs conter-clockwise, find #1 on the cap and work backward going 1-3-4-2. You might be in time since you say the engine runs on gas. This could be because you said you moved the gear to get it in time.
Attached is a picture of the pump on my 46 MD when I got it in 1968. It should be the same as your 47 TD6. I would drain the oil and then add until it comes out of the test plug. If it is full of diesel, it could be that the previous owner just drained it until it no longer came out of the test plug. Until you run it for a while, you won't really know how much diesel gets in. They will all leak a little. When I used my MD, it would gain about a 1/2 cup after running all day. Just ask if you have more questions. Al