id be-wary of advancing pump, the 1 thing, the 'clacking' seems to indicate an advanced timing, already, the smooth out 'when' you pull cold start advance, doesnt mean timing isnt currently over-advanced. the injectors not being pop tested is 'a possible' problem, but your getting too much symptoms of what sounds like it may be an advanced pump. i tho have good exp in timing a motor. you need some timing tools. for a veedub 1.6; a socket +1/2 ratchet, cam lock+feelers, that will handle cam timing, check that 1st, then you need the dial gauge and adaptor, and get pump measurement @TDC. i dont have a lot of exp in a running motor,adjusting pump timing, but right now id say you need to be careful of an over-advanced timing right now, 1 thing some people have pointed out on a 'rough' timing setting, is with motor running adjust pump, try retarding where you are at now and try to find a good smooth running spot/curve, you ll have to loosen injector lines prob a couple of times doing this. if you know how to do it; but its more of an idea, or suggestion, if your not confident in your Diesel mechanic skills, i mean dont burn it up or lose something, cause your eager to jump in to this and if something goes wrong it can become a project. i mean your messing with the timing right now,
if you do a running timing 'try' id still suggest timing cam and pump with right tools before too long; in this case you dont have to loosen anything (at first) the 1st thing you want to verify cam and tdc, and then get a measurement on inj pump, and go from there.
not to say to do adjusting (of timing) you ll need to pull a few more tools out of your tool box, or otherwise be prepaired. as far as van suggestion of pump being 180d out, most pumps that are 180d out have two holes that can take inj pump timing lock. quik way to find out, find crank TDC, and with cam @TDC(also) slip pump lock in, that is the 'general' inj pump TDC, then after a few steps, you get to adjusting inj pump with a dial.