You can try both methods, cores separated and cores stacked. Cores stacked approximately double the CM impedance. Separate cores -- CM filters in series -- also double the CM impedance. Don't worry about windings overlapping. Try with and without. RFI fixes are often all about experimentation. On my router I have one FT240-43 cores on the DC power and on the Ethernet cables with about a dozen turns. It fixed the issue of transmitting knocking the router off.
I would not apply any fixes, such as capacitors, directly to the AC line. That will not provide CM impedance and it must be done with Y-type safety rated capacitors. A large cap such as 0.1 uF will draw enough line-to-GND current to trip an GFI circuit breaker.
On the router ferrites on the AC power and on the Ethernet cable(s) can be a solution.