So you're looking for a pair of shoes that look like Madoka's but are black?
If you want to go with imitating the shoes versus buying really expensive lolita-styled/cosplay only to paint over them, all you really need to do with those Mary Janes you found is paint them!
(Like, if you don't like the black that they are, paint over it until they are at a point that you like.)
I've seen some cosplayers cover the shoe with primer before painting over it but as you can see in this video by Axeceleration Cosplay
, painting over it with acrylic mixed with fabric paint works just as well!
After painting the shoes you can choose to spray some clear acrylic over them if you want to give them a glossy finish but that step isn't really necessary unless you want that touch.
You can also refer to this older Forum post about painting shoes
and see if anything there helps you~
I also found this blog post about how a cosplayer made her shoes for a Sakizou cosplay!
She used the process of coating them in Gesso before painting over the shoes.
For the bow on the back you can just find a fabric bow(or make one) that matches the black that you used to paint the shoes!
For the third strap that goes above the crossing pieces on the ankle, you can just make that from an elastic band painted to match the shoes/bow.
Other than that, your best bet would be simply digging through more lolita-style based websites until you find a pair of shoes that you like at a price you can afford or do as I said above and find some shoes that were made for a magical girl Madoka cosplay and paint them black.