I suppose to do what I think you're suggesting, the current lines would have to be slewed over between the two tunnels, and the current flyover shifted as well (by the time you reach Finsbury Park you want all the tracks grouped by direction, whilst at the junction you want them paired by use)
Yes. Basically correct.
Keep the tunnels immediately north of King's Cross as they are now.
So configured like... Dn S, Up S, Dn F, Up F
After the tunnels, slew the tracks over and use the existing abandoned tunnel (and the middle tunnel like now). In the space between the tunnels put the up slow on a new viaduct over to the far east. The same as it is now except that the viaduct is between the two tunnels rather than after both of them.
At the entrance to the north tunnel the tracks would be configured like this...
Dn TL, Up TL, Dn S, Dn F, Up F, Up S (the ECML now configured as required)
The two tracks from Thameslink now use the spare west tunnel. After they exit the tunnel the up track uses the existing (but may be modified) viaduct to become the most easterly track (yes - crossing over all 4 ECML tracks)
So as we approach Finsbury Park the tracks are configured like this...
Dn TL, Dn S, Dn F, Up F, Up S, Up TL
This means the the two TL tracks have not crossed (on the flat) any of the traditional ECML tracks. The two lines from Moorgate would join between the slows and TL tracks on each side.
Connect the Dn TL and Up TL to the new upgraded goods lines between Finsbury Park and Alexandra Palace and then send the trains on the loop to Langley Junction, joining the Up and Dn slows.