Who is the main character? (spoiler!)

[hollowleviathan]

And another bit he touches some glowing organic material, it makes him flinch and then says wow, it doesn't hurt anymore. What did he mean by that?

This one is rather puzzling, yes. The actual mechanics behind it.

The rest are answered through the game.

I have just one theory.

Spoiler below!

The WAU must have taken note of Simon's body construction prior to taking damage from a proxy, and since it has the guiding mission to preserve all life it encounters, it repairs your body.

Since the WAU is known to emulate what it sees humans construct, these health flowers could simply be it emulating first aid stations.

While the WAU may already known the intended construction of Simon-2, since presumably it built him, it's less obvious that it would know the intended construction of Simon-3, although it was based on Simon-2's design, so it's easy for me to believe that it could correctly rebuild it based on observation or assuming similar construction to Simon-2.