Here's an update guys. I've spent the last few days tirelessly butt dynoing my bike and I've had some great success! Believe it or not, it was much easier than getting the pods to work. I have a little bit of minor tweaking left for tomorrow; my system is running ever so slightly lean and as a result, takes some time to warm up because it runs well.
Here's the info on my carbs now. Pilots went from 45 back down to 42, mains went from 142 down to 90 (stock) and my adjustable needle I set to the richest setting (may need to shim this tomorrow).
It's amazing how quickly one can achieve a proper tune when taking a systematic approach to these things.
My conclusion on this whole debate is this: if you are a regular street rider like me and don't do any racing, save for occasionally releasing the inner speed demon, air box is the way to go. Best all around performance and ease of tuning, as many others have already indicated. Pods look great and all and are easy to remove, but trying to account for the air turbulence is a nightmare. I can't speak from experience about stacks, but from what I've read and heard form others, keep those strictly as race mods only, in a situation where the engine is constantly being tuned, cleaned and tweaked.
I easily spent over a year and a half tweaking my K&N's trying to get them right and only ended up with maybe 70% of my bikes power. After two days of fiddling with the air box, I've gained back another 20% power, and after tomorrows tweaks, I fully expect to be back to full performance again. I hope this is beneficial to all other newbs out there wondering the same thing I was.
If I ever get the time and money to afford putting my bike on a dyno, I will post my results here with a fully breakdown of analysis.