Say i have 3 vectors (Left, Up and In)representing a rotation matrix that is my spaceship orientation. And a vector (Pos) that represents position in 3d space.
How do i adjust the position vector to move the spaceship forward along the local z vector?
Maybe you could try drawing 3 GL_LINES from Pos to Left, Up, and In (in red green and blue) to make sure that In actually faces the direction you expect it to.
If you have already done this, then some more of your source might be helpful.