What should I be looking at for around $1000?

We are about 4 hours east of you. We have a WS Zephyr 160, Prijion Kodiak, Venture Easky 17, Swift Labrador in your price range. They will not be on Craigslist in NC, till the spring.

Aslo, there is a very good kayak shop in Greensboro NC. They are about 90minutes away from you. They have new and used kayaks… They have one of the nicest showrooms around.
http://shopgetoutdoors.com

There hasn’t been talk about river conditions - how fast is it flowing, is it white water, etc? That will impact the type of boat you want.

The boat you are currently using is recreational class kayak. To carry gear and get better tracking, a touring boat would fit the bill. But they don’t do well in white water (neither does the rec boat). Experienced paddlers can do it, but not for the faint of heart. Touring boats are usually used with a skirt, but you don’t have to. And if you are always close to a shore (as you would be on a river until it gets large), rescues could be as simple as swimming to shore and draining 9same as you’d do with a rec boat). But learning deep water rescues would be very good to do (something generally not doable with many rec boat).

I would step back and start with some lessons before buying. An intro to sea kayaking class would teach you the basics, including the on water rescues. Should also give you info about boats design and help guide you toward the right boat for you. This could save you from buying the wrong boat, so save you money in the long run. Could even be worth it to rent a few times after you take the class - try different boats and see if you can figure out what works for you. If you are willing to consider new, many dealers let you rent and then apply the price toward the purchase of a new boat. New plastic sea kayaks are in the price range you are after.