Holes in S4S

Hi. The issue you're seeing are not holes but the remnants of the original mesh poking through yours.
Your blend file contains only one meshgroup while the original package had multiple. So when you import the blend, only one meshgroup is being replaced. You need to either clone something that is made of one meshgroup or split yours the same way the original was split.

That said, there are a lot of issues with the garment. I will list them but, instead of fixing them right now, it would be best to watch a different tutorial and make a different item (tank top) to make the process of learning either for yourself.

- clothing with loose sleeves must be made with arms down, otherwise the mesh will look bad in-game (orange arrow). This process is not beginner-friendly;
- see how badly the garment is shaded and even has holes in some places ( white arrows )? This is the result of using Decimate modifier. Never use it to make lod0 mesh. Either model in quads and keep Particle distance high or retopologize the mesh;
- export the mesh as weld or remove the doubles. The mesh must not have doubles when you transfer weights, it will result in gaps in-game;
- speaking of Shading, either disable Auto smooth or set it to an appropriate number, not 0. This jaggedness of the mesh will affect the baking results;
- there is a slight difference in how bones affect the bottom of the mesh and the top of the bottom, so i assume you've chosen a reference that is too short. Choose the one that is of the same length as yours or a bit longer or the garment will clip into bottoms;
- transfer uv_1 and weights with Nearest face interpolated;

- the mesh is vertex painted with the wrong color. 3fff00 is meant for the skirt-like bottoms and sometimes the breast area. Yours should be vertex painted with 00ff00;
- do not scale uv islands individually unless the difference in quality is acceptable. For example, you can make the pull tag's uvs bigger but the hoodie's uvs must not be scaled individually;
- you should delete parts of the body covered by clothing more carefully;
- bake texture after making sure the item works as intended in-game, otherwise you might waste your time