I Have a downpipe that is 3" but at the turbo it bottlenecks to 2.5". Would this cause over boosting on a stock turbo2 engine?

 

The reason they do that is because a 3 inch pipe won't fit on the flange and they have to squeeze the pipe at the flange to get it to connect to the Turbo.
Still I can see your exhaust flowing more freely than the old 2.5 inch pipe..so I'd say ya..it is a factor.

 

Thank you !

 

Yes, it will cause a significant boost increase if the rest of your exhaust is free flowing.

Port your wastegate. It will help considerably, but may not totally correct the situation.

 

Thanks. I have a muffler as well that I plan on putting on the car. And soon I will be going to a standalone

 

I would worry if you had a s4 turbo. The s5 model has less issues, but porting wouldn't hurt