Yeah with awkward shapes sometimes scaling (S) and scaling along the normals (Alt + S) wont do the best of jobs. First of all check if your scale is applied, because if it isn’t all those operations wont work well. Then try recalculating your normals, if you have flipped normals that might also disrupt your scaling operations.
If nothing works, you can always do that manually. So you can select the edges you want, extrude them, then you can G to grab those extrudes edges and lock an axis, for example X and then enter the value you want to move those edges by and you can just repeat that all around.
Another thing you can do is duplicate the top part if you want it identical to the bottom and then just merge the vertices or adjust them if needed.
