Engine problems

I took a ride the other day and my 08 1250 ran great. Had a coffee and on the way home it wouldn't idle properly and had a miss. It was stumbling under acceleration and I thought it was going to quit. It sounded like a cylinder was cutting in and out. Still doing it at idle. It wouldn't run right until I hit about 3500 rpm. I changed out the rectifier/regulator with a MOSFET unit, because there is another recall on my bike for the R/R... again. I'm getting 13.65 volts at any rpm. I thought that if it was a plugged fuel filter the condition should get worse with rpm, not better.
Any comments and observations appreciated.

build up of gunk in the internal fuel filter on the bottom of the fuel pump and also stuck in the regulator in line above the pump appears to be the most likely cause after a quick google search.

I am going to pull that today. I'll be surprised if that is it because it doesn't get worse with rpm and you would think the higher demand would make it run worse. Anyway a good place to start. Thank you.

I have had my 2007 Bandit not idle right and stumble when I first start it and when it has done that I just shut it off,turn the key back on and let everything re-set and then it's ok again,I'm not sure if it's the ignition ECU not setting correctly or what or if this is whats happening to yours and it's only happened to mine once in a while and it has never stayed that way and always clears up after I re start it.

No, mine keeps acting up.

As it turns out my rectifier/regulator happened to go south right when my rough idle and low rpm stutter showed up. I was indicating a max output of 12.6 volts and I thought the low voltage had damaged the ECM. I'm tired of taking my bike to a dealer just to have them put on the same crappy rectifier/regulator under recall. I bought an aftermarket MOSFET regulator/rectifier and I'm getting a steady 13.75 volts. The engine issues turned out to be one of my brand new Autolite Iridium plugs had failed. I replaced them with standard NGK CR7E's and my bike is running smooth like a turbine again. I should know better than to use anything but NGK. I have a set of the NGK CR7 EIX Iridiums on the way.
The lesson is, start with the simple stuff first.

WOW,that's good news,I guess you just never know but it's nice it was something so simple,I have also had a plug fail once a long time ago on an old harley sporster I had,they were champion plugs and it was only running on one cylinder,rough running and a big power loss because it didn't have much to begin with.

I had myself sweating bullets thinking the ECM got cooked......they are $1500.00 and nobody has one, it would have to come from Japan! I once again have a smile a mortician couldn't get off my face!

Thanks to everyone for the help....it's appreciated!

Thanks for the heads up. So far, 80K+ miles and no problems.

I had exactly the same thing happen a few years ago..

My bike has started running not so good at low rpm so am going to change the plugs again as it's 7.5 k since the last change.
7.5k is the recommended mileage for a plug change in the service manual.

My bike has a Dale Walker stage 2 kit on and others have mentioned it makes the bike more sensitive to plug condition.. this was my finding.

When i last had problems i removed the stage 2 kit and the bike ran fine,put it back on and issues again. Changed the plugs and bingo.

The autolites from what I recall have issues randomly even on other bikes. Do NOT use them just stick to the factory NGKs and you'll be good! Not on purpose but I've gone over 20k on a set and NO issues but boy did she run nice with new plugs again! And being electrical, higher over 15 volts will kill the ECU before under 13 but above 12 volts will!