there are not 3 timing marks to begin with, only 2. the pump turns at crank speed so the pump is either timed correctly, or it is 180 out when the 2 marks are lined up. if you have 3 marks lined up (one of them under the shutoff cover is NOT a timing mark) it will not run correctly. sounds like you understand the indicator mark is just that, and is 1 tooth to the rear when the rest are timed. but this still alows for the crank to be out 180.
so if you have 2 timing marks lined up and the red tooth showing 1 tooth to the rear when #1 is at TDC compression stroke, ie #6 valves have clearance, that should run, but there are several little pitfalls. classic not wanting to idle, but running over, say, 1000 rpm is worn out HH piston. did this truck ever run when you had it or is it new to you? since the bottom cap was off the piston, that may indicate it stuck, and that may have been from dirt or lack of fuel. either would have been deadly to the piston and bore.
if the booster pump is working, and it almost always is, it will self bleed quickly as long as you have removed the bulk of the air from the primary filters.
