How do I fix the meshes overlapping? (Blender noob)

Hi. Just so we are clear, the legs that are poking out must not be touched because they are not a part of shoes.
What you need is to clone boots, not the highest available, the medium. Then export the blend. You will see two meshgroups: the bottom part of shoes and the top one. Splitting shoes into two meshgroups and assigning them corresponding (to originals) cut numbers will prevent them from clipping into pants.
So, you can use these maxis shoes as a guide on how high you should raise the shoes mesh.
Import the shoes, then try to align the shoes’s top with the maxis’s shoes top. You must do this in edit mode, not object mode like right now.
So select the shoes, press Tab, select the whole mesh with A. Switch to orthographic (NUM5) side (NUM3) view. Press G and move the mesh up until it reaches the top of the maxis shoes. Then you may need to make them smaller or bigger and move them to the back. Switch to the front view and align there as well.

If you will find that this - resizing and moving the whole 3d model - is not enough, you should watch any ts4 mesh editing tutorial to get a better idea of available options and what you need to do before using them.