Aftermarket warranty company Transmission work

black night

I am brand new to the Z world, and I have been doing as much research as I can. I bought A 2009 370z with the touring package. After learning about synchro issues, CSC issues, and other things that come up. Carmax sells cars with a 30 day bumper to bumper warranty. I felt every bump and odd shift and took it in to get work done. After a long fight, they are now replacing the flywheel, clutch, and CSC. I asked them to use z1 motorsports sport street clutch and single mass medium weight fly wheel. They are also cracking the transmission as the synchros seem damaged in the fourth gear shift.

My question is, are there any aftermarket routes for transmission rebuilds, because the shop has outsourced the work to a transmission shop in town, and are there any other areas I should make sure get worked on before my 30 days is up?