I did not understand stanzas 1, 2, 5, and 6 in "Lament" by Gillian Clarke.
The copy of Clarke's "Lament" I have access to does not have stanza divisions, therefore I can only make a reasoned guess at what you are calling stanzas. Starting with what I see as stanza one,
For the green turtle with her pulsing burden,
in search of the breeding ground.
For her eggs laid in their nest of sickness.
the explanation is fairly straightforward. Turtles lay their eggs in the sand of their habitat beaches. If the sand has been polluted by ocean "junk" debris and made impure, then the turtle may be said to be laying her eggs in "sick" sand, or a "nest of sickness."
"Lament" is a poem of grief for ... all the things enumerated in the stanzas. In fact, the word lament in the title serves as the first word of each sentence that begins "For ...,": e.g., "Lament" ... "For Ahmed at the closed border." In stanza two,
For the cormorant in his funeral silk,
the veil of iridescence on the sand,
the shadow on the sea.
Clarke is grieving the great bird called a Cormorant that spreads its massive black wings to dry them, looking in its "funeral silk" feathers and iridescent "veil" like the watcher at a funeral "on the sand"--perhaps the funeral of the turtle eggs in their "nest of sickness."
Stanzas five and six add the cause for the lament Clarke is singing (poetry is traditionally considered the poet's song). In stanza five, one cause is the metaphoric representation of war, "the missile's thunder." Another from stanza six is "the stink of anger,” which is presumably the inciting factor for the "missile's thunder." Stanza seven laments the results of the causes revealed in five and six in the lament ...
For the burnt earth and the sun put out,
The scalded ocean and the blazing well.
For vengeance, and the ashes of language.