you numberless infinities Of souls, and to your scattered bodies go, (lines 3-4)
At first, all of the dead souls are lumped together as one group. They have not been separated into the damned and the saved.
All whom the flood did, and fire shall o'erthrow, (lines 5-6)
The Biblical flood was almost like a mini-Apocalypse. God judged humanity and decided that only man (Noah) and his family were worth saving. Afterward, Noah asked God to be more lenient and not come close to wiping out mankind again. According to the Bible, people now have until the end of time to prove themselves. This line refers only to bad people – the ones who get "overthrown."
All whom war, dearth, age, agues, tyrannies, Despair, law, chance, hath slain, (lines 6-7)
These causes of death make no distinction between good and bad people. Good people are just as likely to die from sickness as bad people. The one interesting group is those killed by "despair" – does the speaker seem to take the stance that suicide leads to damnation?
and you whose eyes, Shall behold God, and never taste death's woe. (lines 7-8)
Donne could be talking about two groups here. He could be talking about all good people, who will never taste the sadness of eternal death, or about those good people who happen to be alive on the Day of Judgment, who will never taste earthly death.
for that's as good As if thou hadst seal'd my pardon, (lines 13-14)
Donne compares divine justice to an official document in the realm of justice on earth. These lines are like the old adage, "Give a man a fish, and you feed him for a day. Teach a man to fish, and you feed him for a lifetime." If God teaches the speaker to repent, it will be like having a pardon for all his past and future sins.