The side panel filter you describe is "Stage 3", not "Stage 2".
The "Stage 2" setup, which is probably the best starting point, is the DNA air filter (stage 1) and airbox intake top (stage 2). This setup requires a fuelling device such as Kev Mod. Without a fuelling device you will need to fit the DNA restrictor insert into the stage 2 cover.
DNA Air Filter -
http://www.e-dnafilters.com/Product.asp?ID=810
Stage 2 Airbox Intake Top -
http://www.e-dnafilters.com/Product.asp?ID=824
Restrictor -
http://www.e-dnafilters.com/Product.asp?ID=1243
Stage 3 Side Cover -
http://www.e-dnafilters.com/Product.asp?ID=1211
The above parts will fit all XT660Z and XT660ZA models from 2008-2013.
The only problem you may have is where to fit the Kev Mod under the seat on the ABS model as there is no space spare because of the ABS pump and pipes!