It's not totally clear on the OTR website - they kind of imply that if you fit the side cover (with no other changes) this equates to Stage 2 (which it may well be equivalent to), but that isn't what a Stage 2 set up actually is. Here's a rough guide (in pictures) that's hopefully a bit clearer:
        
 
         
        
 = Stage 1
         
         
        

 + 
        

 = Stage 2
         
         
        

 +
        

 + 
        

 = Stage 3
         
        
 Removing the snorkel effectively does the same job as fitting the Stage 2 DNA airbox top.
         
        
 There is also a restrictor insert you can fit in the Stage 2 top cover to effectively make a Stage 1.5, which would be as far as you could go with out modifying the fuelling to suit.