Oh my, i've got lots to catch up on after being away - welcome from another Chicago Bueller!
A couple things..... 1) opening up the inner airbox is common on the list of first things to do upon purchase. Fortunately for you, he bought a cleaner cover instead of taking a hole or reciprocating saw to the OEM. 2) odd to open up the air cleaner (on a non translucent bike) and not go with a high flow filter. That's not OEM or K&N; I don't know who makes a white/black xb filter like that. 3) XB12 actuator delete is also one of the first things most people dump 4) generally speaking, opening the air intake while leaving a stock muffler is fine as it's within the compensation range of the ECM.
You're probably not getting much out of the PO's mods except more airbox noise but I wouldn't worry about the mods without corresponding retuning.