DDR2 clock is only one of many possible EMI sources. I would also suspect RAM and processor power supply nets, RAM control, address and data lines.
Is it a discrete RAM or RAM module design? Are you sure to have suffcient power supply bypassing?
As a first step, I would try to localize the strongest interference sources with inductive or capacitive probes and SA. There may be a problem that the ground plane is excited and radiating as a whole, but you still be able to find "hot spots" that are the primary interfernce source.