You're using the wrong tool, that is a crimp for insulated connectors. You'd want something that looks more like this;
I'm using this tool:
https://smile.amazon.com/gp/product/B01LH3SR1C
With these pins:
https://modmymods.com/mmm-atx-female-pin-5-pack-mod-0116-3966.html
Looks like adjusting might help, I'll have to give that a try. I'm still not sure if I should be using the 0.5mm, 1mm, or 1.5mm die though.