I recall installing a 3/4" nail down floor 5 yrs. ago over a 3/4" plywood subfloor with the trusses spaced 24" o.c. There were the same "dips" between every truss like you're encountering. When I asked the builder about it, he said that is what the architech specified and that it met code.

Man, was that subfloor bouncy between the trusses. Anyway, back to your problem. Use a long straight edge to accurately flatten the floor. Try using cheap 3 tab composition roofing shingles or roll roofing to build up those low spots. You can staple it in place with a good hamer tacker. I'd put the mineral coated side down on the subfloor. 30 lb. felt will work but since it is thinner than roofing, it'll take more layers to build up. If you have the clearence, you could add a layer of 1/2 CDX to stiffen things up after flattening the suibfloor with the roofing. Good luck.