It's fine to let the topsoil get dry between watering, so you're not doing anything wrong there. I was only meaning that because the roots haven't yet had time to dig their way further down into the pots, the moist soil at the bottom isn't going to do them much good right now. And you also don't want to overwater, as I had to find out the hard way that clones don't like this very much. There has to be a balance, just like the wet/dry cycles of a fully rooted plant, in order for the clone to thrive. This is why it's usually best to transplant the newly rooted clone into a shallow container first, before transplanting into its final pot. It's more difficult to over/underwater that way.

Again, wilting is pretty common when cloning, due to the traumatic nature of the procedure. There are so many things that could be causing it, and I'd hate to recommend a procedure for one malady, and have it turn out to be something completely different that's ailing it. You may have an embolism (an air-bubble trapped inside the stem), or possibly a mold/fungus/bacterial issue, or maybe it's just taking longer than usual for the roots to become firmly established. It can take up to three weeks sometimes for a clone that's being stubborn to vigorously start producing roots.

If there wasn't an abundant root system before you transplanted, then just keep misting and watering as usual, and it should recover on its own...most do. Also, newly rooted clones don't need excessive light, as this also contributes to transpiration. If you're using a HID, moves the clones to the outer edge of the footprint of the light to keep transpiration to a minimum. Good luck, and be sure to let us know how things turn out.