346 - Formae: Hermaphroditus' form, not Salmacis'.
347 - Lumina: Lumina literally means lights, but here it acts as a metaphor for eyes.
352 - Hermaphroditus slaps the sides of his body; this is something swimmers may do before a race.
355 - Vitrō: Vitrō is in the ablative here. You could translate this as "with glass," but "behind glass" makes more sense because it creates a clearer comparison and imagery of a lily in a glass case, just as Hermaphrodite is a beautiful boy in transparent water. He is precious but he will soon be defiled despite the protective case that surrounds him.
358-359 - The polysyndeton here gives the scene an overwhelming and frantic feeling.
360 - Possible hyperbaton; "hac" and "illāc" surround "iuvenī".
363 - Illa: refers to the snake.
367 - Flagellīs: In latin poetry, "flagellis" may refer to tentacles instead of whips.
368 - Atlantiades: son/relative of Atlas. Atlas is a titan and Hermaphroditus' paternal great grandfather.
375-377 - The simile here compares the Hermaphroditus and Salmacis' transformation to grafting, a technique where one takes a branch of one type of tree (usually a fruit tree) and attaches it to the trunk of another, so that one tree can produce two types of fruit.
384 - He "has both of their names" since his name is an amalgamation of Hermes and Aphrodites'.
388 - Incertō: Many versions of this text use "incerto," meaning It is hard to determine Hermaphroditus' gender. "Incesto," however, suggests that this unity of man and woman is perverse and unnatural. It is perverse not because a sexually ambiguous person is inherently unnatural, but because Hermaphroditus was created in a loveless interaction.
Exardō, exardere, exarsī, exarsus: to burn, to kindle
Nitidus, -a, -um: polished, shining
Amplector, amplectī, amplexus sum: to surround, contain, encircle, entwine
Latex, laticēs, m.: water, liquid
Signum, signa, gen. signī, n.: sign, statue
Lūctor, lūctārī, lūctātus sum, to struggle, wrestle, fight
Subiciō, subicere, subiēcī, subiectum: to throw, lay down, subject, throw under
Circumfundō, circumfundere, circumfūdī, circumfūsum: to surround, pour out, overwhelm
Niteō, nitēre, nituī: to shine, to be radiant, sleek, brilliant
Intexō, intexere, intexuī, intextum: to interweave
Flagellum, flagellī, n.: whip, tentacle
Committō, committere, commīsī, commissum: to commit, unite, connect, commence
Conplexus, gen. conplexūs, m.: embrace, bond
Sēmimās, gen. sēmimaris, m.: eunuch, hermaphrodite, emasculate
Incestus, -a, -um: perverse, impure, sinful, polluted, incestuous, lewd
Incertis, -a, -um: uncertain, unsure, doubtful, hard to determine