So i figured out my very own method of making a paper piercing kit. The holes you make would be exa ctly aligned as you want them to!

I have labelled the materials you will need in the above pic and you can use a needle or an all purpose pin for piercing. Most of the things can be made by "stuff" lying around the house!
There's one more thing.. we can also pierce circles by making holes in the diagonal adjacent squares.
---Happy paper piercing!---