Instead of mentally adjusting the notes and trying desperately to please the next guy, just place the notes exactly where they belong. Use your musical gut, not your questioning mind. Your sense of pitch should be developed so that you can depend on your instincts to play in tune.
Don't follow, lead! Find the core of each note and drill it down the center. This should fix your intonation problems.
Our one-sentence lesson: Don't chase the notes, place them!