I agree with the battery terminal being the most likely culprit - EFI can have funny things happen when the electrical isn't perfect. My boat is a DFI 2-stroke and I've had intermittent misfiring that seems to be corrected by a fresh, tendered batter.

However, I think it is also possible you could have had a loose plug wire and when you put them back on it was corrected - I had a misfire occur under heavy acceleration on my RK back after I had just put new plug wires on and checked and found one of them wasn't on all the way!

 

What you are describing it sounds like it's lean on fuel --- pull the spark plugs , they tell a big story

 

I recently had some misfires and some stumbling at random times during throttle travel. It seemed that opening her up and giving more throttle fixed it, so I thought maybe it was the TPS. Then, after a couple days, the bike wouldn't even turn on. I suspected it could be combo of bad TPS and battery. But, following my instinct, I decided to start simple and work my way up.

First I changed the plugs since they needed to be changed anyways. Disconnected all battery connections, had battery tested (it was good), cleaned all terminal and earth connections, coated them all in dielectric grease, hooked everything back up and tightened down with some blue loctite on the threads. Then I unhooked and cleaned all fuses and coated each terminal socket in dielectric grease. Buttoned everything up and she fired up quicker than she's ever fired up before. No stumbling either, although I'll be keeping a close eye on that as TPS is a common issue.

As others have said and will say in the future: start with the battery and all connections.