Riding to work bike with no problems acts like

Hmm. I had a similar issue with my bike years ago and it ended up being the coil.

I had what sounds like the same problem, on mine the problem was the stator not putting out enough juice.

Hello
Your running out of gas.
the fuel filter needs replaced.
your fuel filter is clogged and isn't letting a full flow of gasoline through.
change your fuel filter.

Also check to make sure your gas tank vent isn't clogged.
a clogged gas tank vent with pull a vacuum and try to **** your tank in, but it can't, so your fuel flow stops if it can't breathe.

That should take care of your problem.
have a great weekend
Big Al

Did your bike set up over the winter or for a long period of time (overtwo or three weeks)? If so, the fuel/ethanol mix has gummed, partially closing off jets and passageways. Rather than go to the expense of tearing the carb/injector down, purchase a can of SeaFoam and pour half the can in your fuel tank. Ride the way you normally ride, and if that was the problem, you will notice a difference within thirty minutes to and hour of riding. Might check your aircleaner for cleanliness, also.

sounds like the problem is your battery is not charging when you are riding. The most common cause is a faulty regulator / rectifier. Contact a motorcycle wreckers for these parts, or your yamaha dealer.
Easy way to test is, when your bike is running, and the lights start to dim, before the bike shuts down, using a volt meter, test the voltage at the battery terminals, should be about 14V. If faulty rectifier,no charge going in to your battery, then the reading will be low, about only a few volts. If you dont have a volt meter, then any mechanic shop can do this test for you. best to have this done before buying any parts.

Not sure exactly what the problem is but if I had to take a guess, I'd say that it is running lean and once it's good and hot, it's just a bit too lean to idle correctly.

The bikes come jetted or mapped, depending on whether its a carbed or fuel injected bike, on the lean side to meet EPA emissions standards. The addition of the V & H pipes probably made the situation worse.

If it's a carbed bike, you need to change the low speed jet up one size and add a 0.020" inch thick washer under the needle. Try just changing the jet first.

If it's fuel injected, I don't know because I don't work on the injected model bikes, you'll have to take that to the dealer and see if they can remap the fuel system control for you.

The display is really FI as in Fuel Injection. The fuel injection computer has sensed a fault in the Injection system. You will need to ride the bike to a dealer and have them read the fault codes. It is probably just something minor. Major faults will not allow the bike to run. You will not hurt the bike if you ride it.

Can I get a “very helpful” rating on this answer?

sounds like the fuel filter needs to be changed. It is letting enough fuel thru to idle but not enough to run.

I HAD THIS PROBLEM. BIKE WOULD START AND IDLE NO PROBLEM. WOULD GET UP TO SPEED AND DIE. WOULD START AFTER SITTING. BIKE HAD BEEN SITTING FOR A PERIOD.

FIX:: REPLACED FUEL FILTER FIXED THE PROBLEM.

LOCATION::: TUCKED UP ABOVE VOLTAGE REGULATER RECTIFIER IN FRONT OF REAR TIRE LOOKING UP.