Like MrBill says, an inline filter could restrict flow if it causing a kink in the line, has too little volume/pipe diameter, is put in the wrong way around, or is itself clogged.
It is easy to determine if any of those are an issue at idle, but not so easy to see if there is a fuel flow issue as you get on the throttle, under load (i.e. your 4-7k stumble).
Pods are a nightmare on a motorcycle with little known history, even for guys with a lot of wrenching experience. You really would be better off getting an airbox and starting again, just to get the bike back to baseline. I guess I'd be asking myself why I wanted pods in the first place...looks? Performance gains? Ease of access to the carbs? There are solid arguments against pods with your models on all three fronts.
If you do stick with the pods, you will be in and out of the carbs a bunch trying to get the jetting spot on.
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