Help! 2004 Malibu Maxx - 24,000 m - Needs the trans rebuilt?

My 2004 Malibu Maxx - still under warranty - has been at the GM dealership in Floral Park NY (Hudstead Chevy) for over 40 DAYS!!!! After several feeble attempts at fixing the problem of a rear-end kick when the car changes gears, they finally decided that the transmission needs to be rebuilt! My questions:

- Will the car be the same? Will the process of taking the car apart to fix the tranny affect the cars long term performance?
- How long should it have taken them to fix this problem?
- What type of compensation can I expect from GM for taking so long to fix the problem? Is it reasonable to expect GM to extend the warranty as compensation? The dealership offered a car rental only after the car was out of commission for about month. At the same time, they kept leading me on about how long it would take to fix.
- How typical is this problem?
- Have you ever heard of a car taking 40 days to repair?

My warranty is up in 10 months and I have a strong feeling I'm in for a lot of headaches once it expires. I've already had the steering column replaced, and a few other minor problems. All this, with a car purchased brand new. The irony is that I really like the car...

Help, I need some guidance.

Thank you.

Thomas