As for me, my answers are:
According to modern cosmology atoms did not exist forever. They were created through the process of nucleosynthesis. Are we in agreement that modern cosmology is correct in this?
I am definitely *not* in agreement with that. The purpose of this forum is to research and apply Epicurean philosophy, not "modern cosmology," especially on issues that are highly contentious and conflict with logical reasoning as to whether the universe as a whole had a beginning or is eternal. As for my personal views they are absolutely with Epicurus on this one. There are at some level particles that have been around eternally, whether "atom" is the right word for those particles is going to be a question of terminology.
According to Epicureanism gods exist between the intermundia, i. e. between the infinite cosmoi. Are we in agreement that this doesn't go against any Epicurean position?
We are in agreement that the Epicurean gods exist in theintermundia, which is hypothesized to be between the "worlds." I am not sure what you refer to when you say "this" however. The first part of your statement as to the gods existing in the intermundia is no doubt what the Epicureans held.
The existence of Epicurean gods raises the question where they came from. The logical answer to that would be that they emerged from a single divine source.
No, we would not be in agreement here either. The logical answer to any recurring process in a universe that is eternal and had no beginning is that these processes have been going on forever, and that there was never a "first." And to the extent your "divine" is intended to imply "supernatural" we were certainly not be in agreement.