First one, I understand as -2 to the injury table roll every time you roll injury table. You do mean the tough rule? The way I see it, it gives zombie more chance to only get stunned than actually removed from table.
For the second one, by the book, you'd use the zombies you've paid for. I am pretty sure I'd play it with normal zombies, as if they're other zombies, that have just woken up. When I've played this scenario, I've found out it can be a real bummer...if threshold has 1 agent left, he can't win as zombie would keep on respawning before the agent could remove the grave. Also, the zombies keep on coming so I figured zombie respawn should be either limited to 1 figure per turn or you only get 1 "free" zombie per every zombie (to avoid eternal respawning) and perhaps that you can only spawn 1 zombie from 1 grave...things like that. But I have no idea if that'd make it too easy for Threshold. I've played it twice by the book and army with 3 zeds really slowly gets to the agents.