Others have probably given you enough to go on, but here's my take. You are getting too much air and at 1/2 to full throttle the mixture is going too lean.
That's because it's jetted to have the somewhat restricted air flow of a normal air filter. When you took the stock box off you changed that. Add the pods if you want, but you will have to add a stage II jet kit, or if you have changed from stock exhaust you'll have to go with a stage III. There is a ton of information out there about carb jetting. Read up and then go out and test your bike to get the proper jets. Since they are about $5 each it's not very expensive to change them, but can get to be a lot if you keep getting it wrong. Try this to get started:
It's hard to imagine how much a little change in air flow can affect the carb performance. If your pipes have a significant air leak it will make a difference. You can try to cover the carb intakes...wrap a shop towel or something around the pods for a quick, very rough estimate, of what changing the air flow does to the carbs.
good luck.

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