Hello,
1) I don't look at the stackoverflow questions, so I cannot actually tell you how good the response time / answer quality there is. I recommend the mailing list.
2) I'm not quire sure about your setup now. You can load trips direclty into sumo (and will perform initial routing just like one-shot does it.
As far As I understood you used DUAROUTER once to turn the trips into routes and then ran these with sumo.
What I don't understand is why there are ~55k vehicles active in the network after just 2 hours. I would assume that this is a bit too much for Wellingten. I suspect that your network is completely jammed and this is slowing down the simulation.
If you run one-shot.py with default arguments it runs through a list of rerouting-frequencies. The first frequency is -1 which means no rerouting. This could also lead to a very jammed network. However, this would not explain the slow speed at the very start where not that many vehicles have been loaded. Try running the .sumocfg generated by one-shot py with the gui and figure out if something odd is happening.
One thing to look out for is the number of insertion-backlogged vehicles listed in the network parameters (accessible via right-click on the background or with the little green vehicle button at the bottom).
regards,
Jakob