Run the 2.5" tubing - it will match up to the stock throttle body. You'll need to weld or buy a piece with a fitting on it for the BOV or BPV. (they can be found on ebay and the usual places)
You don't have to remove the A/C, but it makes it easier.
It may be easier to run 2" piping from the turbo to the intercooler inlet. The pre-intercooler size is not as critical
Use pipe from your kit to replace the tract from the VAF to the turbo, the stock piece is horribly restrictive.
You may need some odd couplers for the project,
www.siliconeintakes.com should have what you need (No affiliation, but have bought a lot from them over the years - great stuff)
Either way, FMIC with larger piping is a huge upgrade, you will love the difference