Spyder, I'm pretty sure what you say is true.
What makes me sort of consider injector clogging is that it's staying with the same two cylinders, 1 and 4 even when I flipped the coils around. And, the misfiring is throttle-position related, as if, just speculating here, the secondary injectors are not contributing. But that's just guessing.
But then, on a lot of bikes that pair fires together, and I would have to take a deeper dive into the GSXR600 book to know if that's the case with this bike. If so, then it could be reasonable to expect something in the spark-triggering. Except, the manual says that the coils are getting the fire signal.
I'm getting a little more inclined to get a set of coils, but I don't really want to get into the parts-changing diagnosis thing if I can help it.
The fact that this exact thing has afflicted others here and they went way down the rabbit hole chasing it is making me hold short. So far, in my searching the forum, the only successful resolution came from a guy who changed out his coils, I think.
Also, I took a look inside the fuel tank with a good light and didn't see anything particularly frightening, including the exterior of the fuel pump. That's not to say there isn't clogging in the filters, but without a lot of junk showing, it makes me want to think the filters are okay.
Plus, again: the code is for ignition.
One thing about going around in a circle is that you get familiar with where you're lost.