Much of what you are proposing has already been thought of and encoded in things like the "Pioneer Plaque"
The symbolism is done in multiple layers, since the people who created it had no idea of who or what might recover this plaque eons from now (even our remote post-human descendants might not recognize what this is at first)
The two "bubbles" joined by a line represent Hydrogen, and the symbology represents the number 1 (the atomic element Hydrogen), while the joined line represents the transition of Hydrogen in a "spin-flip" transition (i.e. spin "up" to spin "down"). In physics this can be represented as a unit of length or time (the 21cm wavelength of atomic hydrogen, which can be observed by radio telescopes anywhere in the universe, and the frequency of 1420 MHz)
Other symbols include the position of the Solar System relative to various pulsars (the dot in the centre of multiple dashed lines) and a pretty obvious scale comparison of the builders to the Pioneer probe itself.
For comparison to molecular size, you will have to establish some sort of constant which is observable throughout the universe and is easy to figure out. The Hydrogen one is pretty straightforward, using a molecule becomes difficult unless it is a fairly:
a. simple one, like a Benzine ring, and;
b. observable in sufficient quantities to stand out via radio telescope.
Hydroxyl (HO) is often suggested for this reason, and water (H20) is also very common. Various forms of alcohol and even amino acids have been observed in molecular clouds, but as complex molecules the symbology might be open to various interpretations (The Earthlings said what! This means war!).
It might be simpler to code everything in multiples of a simple unit instead.