I just got my 996 turbo and am having a weird issue with the car. It had a very aggressive race exhaust when I test drove it but I had the seller replace it with a Milltek exhaust with a 200 cell cat. Now the car makes the noise when it's revved past 3500 RPM with 75% or more throttle and once the OBC boost meter displays more than .6 bar of boost. The mods on the car are:

Custom 1.1 bar mafless tune from Sam @Bydesign
Milltek exhaust
Billstein PSS10s
997 short shift kit

I don't think that the suspension or short shifter have anything to do with it but am a little worried about the noise and am wondering if it's the waste gates malfunctioning or is caused by the tune. I have the COBB Accessport and am thinking about loading the COBB Stage 2 tune to see if the noise changes or not. Does anyone have any other thoughts?

Maybe?

Dos the car happen to have TechArt or aftermarket X50 Tips that are out a bit far? I remember that being common back in the day. Or boost a leak.

Boost leak or possibly a leak between the turbo and the exhaust. With the stock exhaust at least there are metal o-rings that should be replaced every time the exhaust is unbolted from the turbos.

If these o-rings are reused (or left out) that can account for the noise.

I agree with the above that its a possible boost leak but also worth checking is the power steering pump. If the bearing has gone it produces a whine and although the whine is there even at lower revs its not really noticeable until you go over 3000 revs.

What is the intake setup? If it's filters on turbos you are probably just hearing turbo intake noise that you couldn't hear with the louder exhaust.