If we are talking about stock turbo then yes, the stock intake is fine, but with an upgraded turbo, you need to upgrade the intake, it's too restrictive. You will notice a quicker spool and more power throughout with the upgraded intake.I have stock air intake other than an AFE Dry Flow filter which allegedly may flow a tiny bit more than OEM. As I am sure you have seen here many in the TDI world feel OEM intake sizes/paths etc. are nearly fully maximized already for the maximum power you could squeeze out of a stock turbo.
If, as in your case, you are installing a larger aftermarket turbo than it fully makes sense upgrading MAF and sometimes a bar map sensor upgrade too.
Diesel,
You need to upgrade both MAF and BAR sensor for the upgraded turbo. The BiTDi MAF housing is larger and the sensor inside is better suited for the increase in flow that the upgraded turbo is going to produce. As for the BAR sensor, max psi for the 3 bar sensor is about 45.5, I'm not sure about your turbo but mine is pushing around 48psi, which is more than the 3 bar is rated for.