I had sort of the same problem as you with the formula. A part from I drew the skeletal on top of the molecular in the end. Hopefully both of ours is ok. For the pencil stuff, drawing displayed formula I'm pretty sure will count as a diagram as it's not words, so it should be fine. It'll still be readable anyway, as they scan all the paper the same way so if it comes up for part of it, it will for other parts too (presuming you used a HB pencil)