I'm so sorry for you! What a bummer. I do think the striped top looks really good and unique on you though.
For the skirts, I think the usual alteration is bottom and, if needed in order to keep the shape, sides. It's not a big alteration per say, but a little bit more expensive than just the hem. Also, think of the fabric: is it a difficult fabric, and is this why there are bumps?
IMO, it's always better to get a dress skirt along with its matching jacket, because otherwise it's a hell to try to match the lonely skirt afterwards.
I understand why you made those pics, though! I don't think you did anything wrong, it's just hard to get it right from afar.