This is so unfortunate thing, the MK6 platform is very similar one model to the other, I don't really think you will have a problem,
But I strongly suggest you to get the same gearbox you had before, or keep the current if possible,
Second get close to a really good workshop like Exoticars, City Performance, Ramspeed, etc, only those guys will be able to tell you in an accurate way what you need,
Keep us posted, this is a very interesting project now, I know it's hard, and annoying sometimes but try to enjoy it!
Best of luck man!