Each "cloning" (once per Pokemon), takes only a few seconds, so it shouldn't take more than a few minutes to get off of Wi-Fi, clone them, and get back on. (Saving to get back on takes the longest amount of time, actually.) The last person I did this for actually just brought the Pokemon they wanted cloned, and then the rest of the filler Pokemon they we're going to trade me for the clones, and just waited on Wi-Fi after the first trade, so you could do that as well.