Good timing, I'm going through this as well now.
Personally I would stick with the stock air intake and "maybe" drop in an AFE dry high flow filter. Stock has excellent IAT control, OEM MAF readings and is not a restriction. Not worth messing with it just for sound and the potential for MAF reading issues and increased IATs.
FTP charge pipes get great reviews, I'm going with the CSF intercooler.
The only part I'm debating is the catted downpipe. I'd like the highest flowing catted DP you can buy. I'm not concerned about CEL as that'll be tuned out regardless. (I don't like the sound of catless DP makes or the smell)
I heard the Wagner comes with a 200Cel cat but not sure if there are higher flowing ones out there?
How difficult is the MST V2.0 install?
Cheers,
Chris