pump and filter
1. Pump: your pump has the mark 5Y1, meaning it was first installed on the XT550, with type code 5Y1, so you have the 'old' pump. This is not necessarily bad, but if you have to replace anyway go for the pump of the 3AJ, which has twice as much capacity. I doubt by the way that anything but the 3AJ pump is available. If youy do install the 3AJ pump you also need a different gear to drive it, and a circlip to keep the gear in place.
You have to (carefully!) take the pump apart to check for wear marks etc.
2. Airfilter. If there was virtually no airfilter before you installed the new one it could be that carb settings are now rich, as the new filer has more resistance to airflow. First thing to do is to set the idle mixture screw correctly, see earlier posts. It is located at the bottom of the carb, in front of the float bowl, in the 'pipe'. Careful not to burn hand / arm  .
Auke
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