I put down tar paper, 6 mil poly, and cdx 3/4 plywood cut into 16x96 strips, the plywood is scored at 3/8 of an inch deep on the back side and it is staggered throughout the floor. However in several places the plywood isnt laying perfectly flat, like some of the boards are bowed up or down. Ive never actually seen perfectly flat plywood though. Will this be a problem when i nail the floor down or will nailing the floor pretty much lock everything down and in place?

YAYYY!!!! An easy one: yup the hardwood will flatten the ply.