its a dead simple engine.
After changing the fuel filter for a proper branded one - I would suggest unbolting the inlet manifold and giving it a nice wash. It becomes super oily and partially blocked sometimes. Next you would have to take out the nozzles and have their pressures set to whatever the PSI is stamped on the nozzle holders - usually 135 psi - you may also find 145 psi pressure ones in your car. Diesel engines are heat compression ignition engines - hence require heat to run properly - if the thermostat is missing install it, if its rusty inside the cooling jackets flush and clean it and use any coolant that is recommended for HD diesel engines (the shockwave of detonation at idle foams up regular coolant and erodes away the head and cylinder barrel liner - HD diesel specd coolant does not do that. (caltex works good in diesels)
dont tinker with boost yet - firstly get your engine to proper specs, including T belt alignments, pump timing adjustments (check the cold advance valve on the pump too - it should not be rusted stuck - if it is the engine will be very very hard to start) unlike starting smoothly on first turn.. Once you get it to run start and run easy. Then you can play around with boost and enrichening the LDA on the pump
Do check and double check that the crankshaft pulley gear is TIGHT - it should be threadlocked in place at abt 130 lb/ft - if its loose it will work all the way loose - as its a 3 cylinder (improper balance) and break the T belt pulley and belt - crashing the pistons into the valves.
p.s. using high tensile strength studs and nuts inplace of the head bolts is a good idea. your headgasket will not give away. The original bolts are one time use stretch bolts, reusing them is bad news