This might be an interesting challenge to sort out.
Since many factors changed all at once (auto>standard conversion, new fuel pump, engine internal work), you are faced with a detective's game determining which one is the cause for the trouble. In this situation the way to go is to start systematically ruling out possibilities. May be tedious and slow, but it'll get you to the solution eventually.
First, echoing one of the earlier questions, can you describe again what the symptoms are? You say hard to start -- is that every time you try to start it, it takes a long period of cranking, or just the first time after it was reassembled, or just the first start of the day, or...? Both cold and when restarting a warm engine, or only when cold, or only when warm?
Able to take a video showing a starting attempt, both when cold and fully warm, so we can see/hear?
And you're saying it runs pretty well once it finally does start, but, you also said earlier that it smoked badly after it started. Tell us a little more about what the engine's performance is like when it does start running.
- Smoke?
- If so, When? At idle, or just under heavy load? Smoke when cold but then stops smoking when it warms up, or is it smoking all the time regardless of temp, or only for a few seconds after start then none at all? What color smoke if present, white or blue or gray or black?
- Power? Does it feel like it did before? Better? Worse? Different in some way?
- Other observations? Temperatures? Sound? Smoothness?
A little more background on the work that was done:
- Injection pump replacement and engine cylinder head work: sounds like the engine was running fine before this was done, what was the reason for the repairs? Just proactive maintenance/restoration? Or was there a problem being fixed and if so, what?
- Trans conversion auto to manual: what parts were used? Was it a complete set of Pinzgauer specific transmission/drivetrain/flywheel/clutch parts? Was it a correct D24T flywheel with the TDC mark for timing? Or did the mechanic have to "get creative" in some way that could have meant there's no TDC mark for the crankshaft to use, or he had to make one of his own that might not be accurate? Or parts used from a different vehicle (like a Volvo) for the swap that might be mismatched in some way and throw a timing attempt off the track?
- What's the complete list of engine parts that were replaced? Photo of a work order?
- How were parts sourced? Any chance that some of the specific Pinzgauer parts for its 24-volt electrical system could have been accidentally subbed with Volvo/LT parts for a 12-volt system? If your new injection pump has 12v solenoids in it, then it won't work well. Likewise if the glow plugs were replaced with parts designed for a 12v system, they will not get fully hot and will cause issues trying to start.
As a general rule, difficulty starting is usually one of the following things:
- Glow plug issues (some not working, or a circuit problem, or wrong style/poor quality glow plugs)
- Injection and/or cam timing wrong
- Loss of fuel system prime (air getting into fuel pump and/or fuel leaking out and/or severe fuel supply restriction)
- Too slow starter cranking speed (battery/starter/connection issues)
- Base engine compression problem (ring/valve leakage or too thick headgasket)
Each of these potential causes presents symptoms in a slightly different way, though. They all make the engine hard to start but each has its own signature tell-tales from what is observed and when (hot/cold etc). The added details on what you are seeing the engine do will help us narrow it down.