Mesh changes after joining? {SOLVED}

Okay so I recently started making completely new meshes for hair in Blender. I successfully created one and got it into the game, and now I'm making a new one because I know what I'm doing now (for the most part) but I've run into a problem. I made the hair from a bunch of different planes broken up into three layers- bangs, ponytails, and the "rest" of the hair hanging down. Now that I've finished meshing everything out, I figured I had to join the multiple plane layers so that I can just have them in one layer to rename them later on for s4s to recognize them. I've figured out how to "parent" them to one another, but that would mean a separate texture for each. Is that okay? Or should I join the three planes?

I tried to join them using ctrl+j, but that changes the positioning of some parts and the overall mesh changes as well.

photos.app.goo.gl/Hl4TKCj8U62weq4v1

Here's the link to several photos with my problem.