well driving habits play a large part in fuel economy.
from what i hear, various other mods can help as well though. a tonneau cover should help unless it weighs so much as to remove it's aerodynamics advantage. a lighter tonneau cover should help, i'd recommend a hard (but light) one. your exhaust system certainly plays a part in fuel economy, and a better one will increase it somewhat. an exhaust system that lets the exhaust escape as easily as possible should help fuel economy as well as be easier on your engine. a couple other things you mentioned, I really don't have much experience with or knowledge of to say anything.
but good ideas. hope it works out good for you