Do you plan on using the SSD for storage or as the OS drive? I would use the SSD as the OS drive, one hard drive as the scratch disk and the other hard drive for render files (a place to store rendered/encoded files). 16GB of RAM should be fine. As for the graphics card you might want to check the list of supported cards: http://www.adobe.com/products/premiere/tech-specs.html
Of course if the 7990 is new enough it might not be on the list but still work. With the new graphics card you should definitely upgrade your PSU. USB 3.0 is nice to have especially if you are transferring large files to external storage or are using a USB 3.0 drive or drives for backup.
As far as pre-built goes I know it will same some time and hassle but in the end, if you decide on a new computer, I think you'd be happier with a custom build. If you do go with a pre-built I would check out the case to make sure there is room for future upgrades/changes.