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As far as the manual transmission no issues I've ever heard of except you need to leave it in reverse when you park or the battery will die.
He may have been thinking of the differential casing. It was on the weak side in 05 and may break apart if you get crazy wheel hop at the track. It was replaced in 06 with a stronger one. It's fine if your doing normal driving on the street.
There are several 05 owners on here over 500 HP and still have the stock rear with no problems. In fact I've read very few threads about it actually breaking. But it is possible since GM did build a better one after 05. I'm sure someone that tracks their 05 (I don't) will chime in.
I have an 05 (A4) and have been at the drag strip almost every weekend (during racing season, March thru Nov) and make between 4 - 10 runs a day... I'm just starting to have a slight problem with the posi not hooking up both tires I'm only spinning the right wheel on my burnouts..
I think I'll need to get the posi rebuilt.. other than that I have been at the track since 2008 (with this car) and NO wheel Hop or any problems.. (I use Drag Radials)...
Before I bought my car, the transmission was rebuilt. It's an 05 manual. The dealership said the person who traded it in had to tow it in because it was unable to be driven. They said the syncros for first and second were shot.
They rebuilt it, and gave me a 90 day warranty on it. I drove the **** out of it, and drove it hard to make sure I wasn't going to have any issues!
Three years, 15,000 miles, several passes at the dragstrip, and countless spirited pulls on the street, and the transmission has never even so much as ground a gear!
I have no idea what the previous owner did to the car to fry the transmission at 40,000 miles, but I've had zero issues since I got the car.