According to Mini enthusiast site Motoringfile, all orders must be submitted by August 28 in order to get a custom build. Orders are also locked in after that, so if you do get one of the spots, make sure you're absolutely content with the car you order. This cutoff will affect all models of the Hardtop, including the John Cooper Works model.
After August 28, owners will need to wait for the new Hardtop to arrive, which Motoringfile estimates will be in March of 2014. If you miss out on this final allocation of hardtops, all is not lost, however. Mini will still accept personalized orders on other bodystyles, which won't be replaced by F56-based models for some time.