You have the paperwork from the rebuild, but perhaps more importantly, do you have any paperwork from the times you brought it into service.
If you can prove that you've brought it in 5 times for service, than I would take them to small-claims and get all the money back with the exception of the part value, plus the value of any time of from work, rental cars, etc.
If you've given them 5 tries to fix it, you have, in good faith, allowed them the opportunity to fix their mistake.
Just because someone has a warranty on something does not give them the right to have it constantly break and require you to continually allow them to fix the problem.
As it stands, not only do you have no reason to believe they will fix the problem anytime soon, you have no reason to believe the problem will be fixed when your warranty expires. They've essentially not completed the work they said they would. You still have a broken transmission and that's NOT what you paid $3000 for.
It doesn't matter if the warranty is expired. They showed that they were never able to satisfactorily repair your transmission, meaning they never fulfilled their end of the deal.
If you have paperwork showing 5 visits, screw the whole corporate complain thing and just take them to Small Claims. If they're a franchise, the dealer will lose. If they're a company-owned location, they'll settle with you.