Ok, at first the opening narrative was really confusing me, but once I read your description of how the "it" units shifts I get it. Brilliant way to make the objective dynamic and stick to the theme. Well done.
Does this have to have only one deployment map? Couldn't it be used with any of the basic 6 maps?
Does the battle need the flood mechanic? What happens is the flood kills the "it" unit? How is a new target unit selected?
Since the scenario isn't tightly connected to board terrain I think you could use any deployment you wanted to.
The intent of the flood mechanic is to avoid a player hiding the 'it' unit in a corner or at the very edge of their deployment zone, or otherwise behind some los blocking terrain. The hope is that a clever player could use units with scouts or decent ranged units to maybe snipe out 'it' from the beginning. I think if both players agreed to not cheese it to much, then you could skip it.
If a unit is destroyed but not by the opponents unit the opponent designates one of their remaining unit as their new it:
"If a unit designated as 'it' leaves the battlefield without being destroyed by an opposing players unit, the opposing player must designate one of their units as the new 'it'. It must be on the battlefield or otherwise enter it as soon as able."
