CTS cock up from time to time like anyone else, I very much doubt due to time scale they'd do anything, and that would imo be totally reasonable, you never know what the previous owner has done since the rebuild, if indeed it was rebuilt!!
Unless you know for sure any potential s/h box has been rebuilt or is good then it could be a dud as well.
Why not go to some rebuild places and get quotes, they will drive your car and advise accordingly.
My rebuild cost £580, but had done 200,000 miles!!
Every part that could be knackered was knackered, the place I use is not the cheapest but do stand by the warranty, unlike some mode dubious places, not at all suggesting CTS here as they do stand by their work, but many don't.
I've seen T5's go for around the £300 mark on the bay, around the same price as a basic rebuild from some, I know which I'd prefer.
tabetha