It sounds like you first need to do a full bleed of the fuel filter and injection system. It's easy to do, but takes a bit to explain. Even a small amount of air will prevent running or produce very, very rough running until the air purges.
Then, you need to check your glow plugs for proper function. In an early BJ with a B motor you can "touch up" the glow plugs to produce a smoother run while it warms up. Using too much throttle with a cold motor will make it run worse... use just enough hand throttle to make it run smoothly - about 800 or 900 rpm (given that a normal idle is about 650).
Then you need to see if you have enough oil to get the oil pressure up to keep it going. If it stops after about 5 seconds, then you may have oil starvation issues. One solution is to add a few more litres (ie: overfill it) to get the oil pump to prime, then drain the extra oil out once things are going again.
The "choke," or throttle plate, is used to regulate the position of the rack which in turn determines the amount of fuel and thus the speed and output of the engine.
hth.
~j.