I'm confused.
You don't use the crank pulley bolt threads when removing with a tool. There supposed to just slide off tho.
When you use the tool you use the flat piece with the 4 slotted sections and thread the bolts in through the slotted section where they line up. Then the big bolt that come with the kit goes in the middle of the flat piece and then there is a cone piece that goes on that and stops at the crank snout. Turn the bolt in and the that will pull the flat piece and the crank pulley attached to it off.