Pretty much - there's no way to know what the 'stock' fuel setting is; typically you adjust based on smoke. With a turbo, as long as you have an EGT gauge on it, it's a "how much power do you want?" thing, because you can burn the entire maxed-out output of the IP... at least once the turbo spools.
Timing - The only 'correct' way of knowing is to put a meter on it; you can get 'close' by ear - basically, you are adjusting it based on how it drives:
1. The spot where it's most responsive is usually good
2. You never want to see blue/gray/white smoke on acceleration. This is retarded timing. (black smoke is normal or advanced timing, and means too much fuel for the air).
3. Generally, what I find is that you want to hear a little 'diesel rattle' at idle with it warmed up, and you should be just at the point where that rattle goes away at highway speeds. That will be close, and you can fine tune it based on mileage or whatever.
It's one of these things that I encourage, because while you might not make it perfect, "good" is better than "poor" which is possibly where you have it now.
Especially as these pumps slowly get more retarded over time as the internal parts wear. New injectors on a worn IP will instantly give you retarded timing and need some advance.