I am witting this post to get some help!
Three weeks a go I took my car to have the 2nd gear Service Bulletin perform on it and have a Toda Racing flywheel install. It took them three weeks to give my car back after opening the transmission several times.
I still don't have my car working properly; tomorrow is going back to the dealer because it has a winding RATTLE noise on the transmission; this noise gets faster as I accelerate and goes away when the clutch is engage.

They already replaced the clutch and the main shaft bearing that go near the rear axle. They also open the transmission and aling the second gear shim, but the noise still on.

Any suggestions as to what can be?

The car was running great before this.

Please advise.