Can any experts out there help me with an airbox/stock configuration question?

I mentioned in an earlier post that it was my intent to make sure my 2008 Firebolt was fairly close to the stock configuration as possible and within reason. (I'm not going to remove or not perform a mod if it will increase the longevity of my bike plus I like the aftermarket muffler sound) My reasons for wanting it stock are simply that I love vintage even in the mechanical configuration, possibly because, generally speaking not always, I feel like stock is the easiest on a bike, automobile, atv, etc. and its an opportunity to learn about the bike inside/out for future repairs or the addition of beneficial Mods and because it does appear to be running a little lean and will kind of cough every so often like the fuel/air might not be configured correctly.

My bike does appear to have been modified where the previous owner removed the airbox top, cut the harness to the interactive exhaust device and cut the cable to this device as well. I am assuming the configuration of the interactive exhaust device that goes on top of the airbox only worked on the stock exhaust, am I correct?

1. So, lets say I was starting from stock going to where I am now, what would be the minimal change that a firebolt would normally get if you just wanted to add an aftermarket muffler, Jardine, Drummer, etc.?

2. I ordered the airbox top to replace the one missing from mine but is the airbox top going to really do anything without the "interactive exhaust" configuration installed?

3. Does pretty much all owners of firebolts with an aftermarket exhaust do away with the factory airbox top?

My bike is running great just has a hiccup from time to time. I had an independent and well known Harley mechanic change the oil for the first time so he would know me and be familiar with the bike in case I ever had a major issue with a motor rebuild or something like that. When I picked up, of course you get the yack yack about having a Buell but he's very straight forward and has worked on Buell's when he was with Harley up until maybe 05 ish. He said he felt like it was running lean.

Any of you gurus out there that could help me, I want to learn and figure out all the issues above. Thanks!