In theory all those things you mention should be factored into calculating pump head, and every company I've worked with does it differently. Bell and Gossett (or any manufacturer) typically has charts you can use to approx. pressure drop across air seperators, Suction diffusers, etc. There are also many textbooks that you can get equivalent lengths for fittings as well. Very often the piping system is not installed the same way it is designed so safety factors need to be added in the calculations as well.
I use an excel spreadsheet. The main components, in my opinion that need to be accounted for are: Length and size of piping, chiller or boiler pressure drop, control valve, air separator, triple duty valve and suction diffuser and the coil pressure drop of the heat transfer device at the end of the run(reheat coil, Unit ventilator, fin tube, AHU coil, etc). These values are easily obtainable from the manufacturers of the equipment you design around. As for all the fittings, sometimes this is not as practicle to get so I typically take the pressure drop of the total piping run and add 50% for fittings (ie if the piping pressure drop is 22 feet then add another 11 feet for the fittings).
Like I said, Everyone has their own methods, but this method has never gotten me in trouble.
I hope this helps.