Carbon buildup, dirty injectors, dirty hpfp, dirty fprv, dirty rail pressure regulator, dirty rail/hpfp sensors, failing lpfp. Could be a lot of things These are the thing's I'd check.
I know for a fact that when I had my pump rebuilt, the guy over at Vis told me it was one of the dirtiest pumps he worked with. I'm pretty sure my injectors are partly clogged as well. The FPRV was black on the inside when I changed it for the uprated one.