Finding the critical coupling element(s) ought to inform any
layout changes. You might like to try getting the extracted
capacitances pushed back onto a schematic so they are more
readily observable / inspectable. I haven't done that, myself.
The alternative is to try and slog through the analog extracted
view selecting all pcapacitor instances and looking at the big
ones first. You can highlight nets for instance and see whether
any particularly nasty ones are found (like, running gate parallel
to drain for distance will give you Miller-amplified Cgd adder).
You might fine it easier to "hook it up loose" and then pack it
incrementally, checking for phase margin degradation along
the way; the point / feature at which it starts to degrade like
you see in the "present final" layout, probably holds clues.