2009 Kawasaki ER-6N lugging/bogging/stalling when hot and taking off from a stop

Edit/update:

So I finally got around to doing the full service and the air filter wasn't clogged, it was the opposite. The foam had completely disintegrated and whatever bits and pieces of it I didn't shake out of the airbox presumably went through the engine over the course of who even knows how long. Going to guess this is the original filter and it has never been serviced.

The bike was running pretty lean from that paired with the aftermarket exhaust, and a new freshly oiled filter seemed to do the trick. Runs peachy now. Tossed in some new plugs when I was in there since pulling the tank and airbox was a pain in the ass I don't feel like repeating for a while, and half a bottle of injector cleaner in the tank for whatever funk might have been left laying around.

Original Post:

Title, she's idling funny and lugging/popping from a start when she's all warmed up, feels like the engine is very hesitant and it's resulted in a couple of embarrassing stalls as well. The bike runs totally fine when I've got some speed.

My suspicion is a super dirty air filter. Maybe sitting still there isn't enough air going in, and once I'm moving the air is forced in? The slip on exhaust that's on it shouldn't be affecting anything, right? Basically, before I go and start ordering things, is there anything else I should be checking for?

It's the winter months right now so I'm not really able to do much riding in the slush and snow but I would like to try to fix this before it's time to get back out there