Boots - make sure vertices are merged
Shoes- make sure top area is only weighted to the leg bone.
Pants and Tops - Make sure the bottom part of the upper bodies and top part of the pants is only weighted to the hips bone without any influence from spine or upper leg bones.
Still the same issue with all upper bodies and pants. Make sure the part that was red in pic above is completely blue for all spine and upper leg bones.
Here are the files you have on builder atm: spine and spine 1 bones
The bottom part should be completely blue for these and upper leg bone weighting should be completely removed