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I know that if you have a magic ki focus and a magic weapon, you have to decide which magical properties to use whenever you make an attack.

What about base properties (such as high crit or brutal) of the weapon or base properties of a superior ki focus (such as reaching or deadly)?

You keep the base properties of the weapon for weapon attacks, and the superior properties for implement attacks (and implement attacks ONLY).  It's only the magical properties, crit dice, enhancement bonuses you have to overwrite.