You don't need to magnetise the waist - just extend the 'nub' on the dome so as the top won't slip off of the legs (that will make sense once you build the legs if it doesn't at the moment).
I can't advice on the faces, as I didn't do that, but for the Thermal Cannon / Battle Cannon I used 2mm by 2mm magnets for the Battle Cannon (embeded in where the circular sections of the gun mount touch the main section of the gun), and 5mm by 1mm on the end of a rod that runs through the main section and into the Thermal Cannon.
Honestly, I think I over-complicated the Thermal Cannon, but it works.