Dies/will not Idle but runs Fine at 55mph

Sorry about the long post but wanted to give yall all the facts.

Yesterday I decided to ride my bike a bit because I have not run for more than 15 minutes in about 2 weeks. Started right up, I rode around the neighborhood and stopped at a friend’s house and he noticed my registration sticker was expired, ( new one is sitting on desk at home). I went back home, I took off the plate to clean it and put the new sticker on, (20 mph speed limit 9 min. ride total). Rode perfect like it did the last time I rode it 2 weeks ago.

Got back on, rode out of the neighborhood onto 50 mph road and have slight hesitation like usual when cold and just of idle throttle position when accelerating or letting off, I go ½ mile and make u turn under freeway and start to accelerate and have stumbling/jerky hesitation for a few seconds then smooth’s outs and run ok for ½ mile then dies going 55. I try to bump start before coming to a stop but no go. Pulled to shoulder and cranked and finally got it started but had to keep it in higher revs to stay running. Made a u turn and went back home.  

First thought is older gas, (shell v power 93 with marine stabil in it but probably 4 months old).  Sipon most of the gas out and put in ½ gallon of some newer gas I had on hand for the boat. Start it up but will not idle but will run if revved past 2000 rpm or so, (just like before).  I decide to try to get on the freeway and run it.  Make it on the freeway and runs perfect if going 40- 75 mph. Pull off freeway 8 miles down the road to fill up with fresh 93 shell and it dies 250 feet from the gas station. I push it to the pump and fill up. Now will not start.  So I let decide to let it cool off as I do not want to run down the battery. Wait 15 min and I get it started but it dies and notice if I turn the throttle hard to the off position is will start but then die. Put the throttle in ¼ turn position and crank awhile and it starts and will keep running if kept a 2000 rpm or over. Get back on and ride 8 miles home and runs perfect if going 40- 75 mph. Have to keep up the revs to get through the 20mph neighborhood.

The fuel pump powers up strong so this morning I unhooked the FMF tuner to take that out of the equation. No change. Pulled the spark plug and it looks good just slightly rich not wet but better than too lean, (I have never pulled the plug before and it was not very tight??). I messed with the idle screw some but no help.   Air filter ok no mice in air box.

So at this point I am stumped. Any help would be greatly appreciated.

Info on the bike is below

2008 with about 4500 miles on it. I bought it last year with 2500 miles and have put 2000 trouble free mostly off road miles, (until yesterday) on it with the mods below;
I replaced the fuel pump when I bought it last year before it ever gave me any problems just to be on the safe side. Other motor performance mods are; FMF tuner, FMF Q4 pipe with power bomb, AIS removed, EXUP removed and EXUP servo motor replacement module, Ultimate air box mod, uni air filter and Speedo healer. Also did the High Five  TPS adjustment, (TPS at 17-100).

Since you removed AIS, I'd check the vacuum lines you capped off?

Since bike seems to run fine at some speeds/throttle positions, it might be some kind of vacuum leak somewhere?

Maybe a rubber cap dry rotted and split a little?

Thanks for the reply,

That is an excellent suggestion as that is exactly how it is acting. I had checked the caps on the air box but forgot about the one the top of the throttle body. Just checked it and it is ok. Did not see anything out of place. I just put some seafoam, (6oz) in the gas tank and rode for about 25 miles going 65-70. Runs perfect above 2000 rpm but still will not idle. Has anyone ever had a throttle position sensor go bad or have air leak at it. It looks ok and no fault code shows. It just so weird that it ran perfect until it missed/stumbled yesterday. It may have backfired some also, is these something that a back fire could damage?

Any chance that this weirdness started sometime relative to making a change to anything?
Like maybe the TPS adjustment?

I wonder if you're experiencing a over-rich condition at low throttle and it's only when you really open up things that the bike runs well.

What settings are you running on your FmF fuel programmer?

I had not changed the setting or made any adjustment for over 1500 miles. Has been perfect.

Ran perfect two weeks ago and same earlier in the day before this condition started.

Did the TPS when I first got it as I could not live with the snatchy throttle as I ride some lows speed technical trails. I did get rid of the snatchy throttle or smoothed it out greatly with all the mods.

The settings are 3-3.5-.5-8-6-4 but I disconnected it yesterday and it still would not idle. I hooked it back up because I did not want to ride with it disconnected when on the freeway yesterday.

Could you try the "taco mode" thing and get the rpm's?

I'm out of ideas.

While at home for lunch I put it in taco mode. The co is 10 and this is how it was when I bought it bone stock. I had a very hard time getting it started today and it died at 4500 rpm when I backed off the throttle. Would not restart and did not want to fully discharge the Shorai Lithium-Iron battery so I put it on the charger and am going back to work. May have time to mess with it tonight.

Thanks for helping!!

Well since this was stumping me and just to take one unknown thing out of the possible problems, I stopped by the Yamaha shop today and picked up a spark plug, (I would have done this sooner but they are closed on Sunday and Monday). I thought I had a spare but I could not fine it anywhere.    

Put the new plug in and it fired up immediately and idled perfect.   Put it all back together and went for a ride and back to normal and runs perfect. The other day when I pulled the plug, I cleaned it and used some 1000 grit sand paper to lightly scuff the electrodes and then re-cleaned with carb cleaner, (it looks great as it only has 4500 miles on it). Before I put it back in I tested for spark and it look ok but obviously it was bad. So anyone with this condition change the plug.

Thanks fo the help Motokid