It really does depend on what's fried. If your computer has front usb ports, try those. If those don't work then it might have fried more then you think. From the sounds of it, it still boots up (seeing as how you posted and managed to actually test the usb ports). If only the rear usb board are shot, sadly you are looking at new mobo or an expansion card to give you more usb slots.
Take a run to your local compu-friendly store and see what they have to say about it. Installing a new mobo can be somewhat pricey and you will most likely lose your configurations and any files you don't back up on an external. The expansion card will simply pop in.
Something like that will be easy enough to install and will give you 4 external usb slots (also for about 70 dollars less then what a mobo would run). Don't mind the internal one, it's mostly used for conversions of old hard drives or cd/dvd drives.