Dave,
One needs to fit the wings only once if you match drill the fairings now while the wings are on the fuselage (otherwise, you have to put the wings on to match drill later, and then pull the wings to install nutplates). Then you can install nutplates and only reinstall wings once more - the final install.
I recall that the fairings are cut pretty closely to correct - at least they will fit on the wing so you can drill them without any trimming. Drill and cleco, mark your trim line and that's it. You can then install the appropriate nutplates on the wing roots after you pull the wings off.
Cheers,
Greg