The transmission in my '99 996 needs some additional repairs and therefore I am considering getting a replacement refurbished transmission rather than continuing with the repairs. Does anyone have any experience with, or can recommend, a good company for refurbished transmissions and is it likely they will offer a trade-in credit for my existing unit?

Try Gbox and Vertex, I know they both offer rebuilt transmissions for the 996. And if you do a search on eBay under Porsche 996 transmissions there are 12+ used, new and rebuilts listed.