i dont think IQ directly relates to your both static,ie- mechanical and/or injection timing. if static timed, that is crank and cam @TDC, pin in inj pump, thats the TDC static mark, set belt tensioner, (there are a few other steps), tighten cam bolt, etc, to turn engine over by hand, at least 2x(@-crank revolutions). after this start up, it shouldnt run *that bad, in fact it should (appear) to run just about normally. you need the vag-com cable and laptop and set inj pump timing. at this point its a guess, correct pump timing may correct the rough running. then again rough running is also an easy symptom of air infiltration in fuel system. other place to check is the pump work that you just did. is air getting in there, the seals you just re-did?
i doubt bumping IQ off the info youve given is a good starting point. either pump timing(re-check your mechanical timing first), or air in pump. seal job you just did. another thing, how long did you let motor run, can take a few minutes for an opened system to purge all the air out. esp if you opened pump, let idle for a few more minutes and see.(??).
the ross-tech cable is a little expensive, to say its more than a little expensive. you can try the partsplace cable if you want. i dont know personally as far as if PP cable works ok, i have a ross-tech cable, so that i know.