Im assuming you are using glue on nocks? I LOVE four fletch, dont think I will ever go back to three.
Few ideas....one glue the nocks on after you fletch. I know when I make woodies, I usually glue them on first, but if you make sure the fit is tight, it should be ok.
Experiment with the four fletch angles(I can think of 3 configurations) until you find your favorite, or the one that offers the most clearance between the fletches and shelf.
Of course, some say that with a properly tuned arrows, feather clearance shouldnt be an issue.
Disclaimer: I know virtually nothing about arrows, just love making em.
Good luck.