if your bike ran fine with factory jetting, but now runs poorly with factory OR larger jets, then jets aren't the issue, some other factor is problem, mainly clogged carbs, specifically fuel circuits.
First, factory airbox and filter is HUGE relative to engine size. It's about same size as EX500, an engine with 2.5x airflow and power. Filter is about same size as my CBR600RR, an engine with 5x airflow and power. Therefore, airbox and filter represents zero restriction and switching it for pods will make zero difference. As numerous people have discovered already.
Major intake restriction is snorkel, remove that and airbox flows as well as no airbox. In fact, that's what I did for one race last year as test. With no airbox at all, I got exactly same times as with airbox with snorkel removed (usual toss fastest/slowest lap, average rest). Which was about 1/2-sec faster per lap at Thunderhill than factory airbox+snorkel.
Also you are assuming factory jetting is perfect, therefore needs adjustment with mods. Nope, it's way, way too rich in high-end (where mains adjust) at 10:1+. Max-power occurs on NA engines around 13.5:1 or 35% less fuel. Here's some dyno-charts of full-exhaust mods.
http://www.racingorder.com/2010/10/t...-dyno-results/
Notice he got +21% more power with snorkel removal and full exhaust with NO jetting changes. Here's actual data from that dyno run. Note with +21% more airflow in top-end, it is still WAY to rich at 11.3-12.1:1 AFR in high-end. That's why Spears Racing suggests 96 mains for even more power. I use 96 on my race-bike with full exhsust (+21% more HP) and 94 on my street-bike with Ali El Cheapo muffler.
The thing with tuning is you need objective tests with quantifiable data in order to see what effects your mods have. It frequently requires multiple stages of adjustments after analyzing AFR data from dyno-tests or widebands.