Mesh overlapping and tiny holes

Hi. For the shirt to not clip into the jacket, they must morph and move the same way. However, since the modified shirt connects to the lower body, you need it to behave like the lower body in that area as well.

I think it would be faster to re-do the mesh instead of trying to fix the current one ( i used new blender, but everything is in the same place in the old one )
- export the original, open, no need in joining meshgroups into one. In edit mode select everything and Mesh - Vertices - Remove doubles with Merge distance set to 0.0001;
- hover over the bottom of the shirt, press L to select, then Shift-select those faces at the bottom. Delete - Faces;

- enable Snapping to Vertex, select one vertex, press G, and move it to the closest lower body's one. You do this everywhere theres a gap. You can create new vertices ( selected in the screenshot ) to join everything better;
- as for the surrounding area, move vertices around so that theres no sharp transition;

- now you need to transfer weights from the bottom to specific vertices on the shirt. Select all vertices you snapped to the body, create a new group, click on Assign;

- expand the rig and make bottom selectable ( cursor icon);
- select the shirt again, add Data transfer, choose bottom as Source. Choose Group in Vertex group. Enable Vertex data and Vertex groups, choose Nearest face interpolated as well. Enable Face corner data and UVs, change to Nearest face interpolated and choose uv_1 in the drop down. Apply;