If you keep looking for prada boots you should find them. I've found them for people both with the zipper and also elastic like the stormtrooper boot. Either way is fine as it gets covered up by the ankle guard and shin guard.
As for modifying the boot, I have had plans to do it right forever but never get around to doing it. I believe the section where the purple is is actually cut out of the boot. Another piece of leather is stitched inside the boot overlapping the holes on the inside of the boot. Then the purple piece is glued into that recessed area. I have a cobbler here locally who said he could do it for $150. When we get around to rebuilding our zam suit and get to the boots I'll probably go ahead and do it.
Another option, which is what I did initially was glue the purple piece on top of the boot. It still looks fine and is an option if you can't find a cobbler to stitch the boots. Cobblers have the fancy stitching machines that go down inside the boot 
As for coloring your boot, use leather deglazer (which is mostly acetone) to remove the sheen from the leather and give the paint a surface to adhere to. You'll then use brown leather paint. Spray it on in several fine layers. It will take a lot so get 2 cans. This is actually how stormtrooper boots were made originally by painting black boots white. I've painted several pairs of boots for folks and they turn out nice and after wearing they whether nicely. After a year our Zam boots looked perfect. You can advance the whethering by using sandpaper or scotchbrite pads etc. to scuff it up.
I hope that all makes sense.
