Most likely carbs were clogged with jelled petrol from sitting around before you bought it. Limiting fuel flow just happened to balance huge jets and coincidentally provided proper AFR. Temporarily... Until further use dissolved an clear out clog and now you've got stable configuration with way too much fuel.
In stock trim, newgens have slightly lean midrange and super-rich WOT/high-end. Intake has no restriction (other than intake snorkel). Removing airbox completely doesn't improve flow any, so K&N pods won't change anything either. Full exhaust does yield a 20% improvement in flow and 20% improvement in power.
My race-bike was dyno-tuned by sponsor Spears Racing after I installed full Tyga exhaust. They found that my WOT/high-end mixture was
still too rich and went to smaller DynoJet 96 main jet and stg. 2 needle. This gave us dyno-chart like this . We couldn't go even smaller main-jet for even more power due to leaning out mid-range too much.
Stg.2 needle is at very bottom (4). Notice that tip is larger diameter than stock needle #3? This has effect of reducing fuel and leaning out WOT/high-end even more than just down-sizing to 96 mains alone. Problem is mid-range lean spot. Can't shim needle because that would also richen top-end. I'm going to custom-grind some needles on mini-lathe
Check out this thread for related discussion. Please read the linked magazine article where they prepared newg en for racing:
https://www.ninjette.org/forums/showthread.php?t=329085