Dust, on a MF back, pretty common. Odds are it's on the sensor, you can pretty much forget looking at the lenses. Even if on the lenses, you would not see it as a spot on your images. Dust on a or in a lens is very diffused, at least with the lenses you are referencing.
The IQ3100, or any Phase One back, is very easy to clean. Phase One has a cleaning kit, 2 solutions. One is a blue color, One is clear. Unless you have a smudge on the sensor, you don't need the blue color, I believe it's called solution A.
In the cleaning kit there is a plastic piece that has two widths. The smaller end is for the cropped sensors, you won't use that side. You just fold a wipe from the kit around the plastic and wet it with a couple of drops of fluid. You can use PecPads, or any pad designed for sensor cleaning. I prefer the ones from Macgroup, but they are hard to find.
I would only wet clean, after you attempt to blow off the back. Use any hand held blower, Rocket blower is the brand I use. Most of the time you can get the sensor clean with this. Only wet clean after a few attempts..
Dust, on MF back, is just part of the deal. You have a huge sensor, a very large opening with the XF mirror box, and a huge mirror flopping around. If you think dust is bad with the XF, try a tech camera 10x worse. At least from my experience.
The huge advantage a Phase One back has is that you can remove it from the camera and have great access to it for cleaning.
Paul C