Hey, I have the same problem. I ride a 98 R1 with almost same mods to it, but mine bugs down at higher speeds when you get off the throttle and them back on it hesitates before taking off. Did you figure it out by any chance? I'm about to take my carbs off to see what is up, it feels like lack of fuel.

LET ME KNOW IF YOU GOT IT FIXED AND HOW.

 

Problems

I have tried about everything that I can think of, the only thing that has worked at all is moving the carb breather hoses around, I am getting so much air under my tank that I think air pressure is hurting those breathers. I am about ready to take it to a dealer. I am at a loss. Did your bike do this when you had it stock??? I think that it all has to do with air.

 

I was reading up on this whole lot and some one said that he had a very similar problem and what it turned out to be was the fuel pump. Even tho it was still pumping it did not have the same high flow that the engine needs in higher RPMs. He said that the flow was almost half of what it needed to be. I am going to get a new filter and if that doesn't do the trick I'll be installing a new fuel pump. It makes a lot of sense; my bike really feels like it is starving for fuel. I don't think it's the air, with or without the fairings the air box is still the same.

And to answer your question I bought it crashed with only side fairings so I just took all of them off.

http://www.r1-forum.com/gallery/showphoto.php?photo=18983&cat=500&ppuser=81827

:fork

 

Mine did that too.. i had a carbon fibre ram air intake system on it and the line that plugs in from the carb to the airbox was not in after a service...

basically at higer speed the air:fuel ratio got all messed up since the air pressure wasn't going to the carbs to allow more fuel flow at those speeds...

your case may be different but check the line that go to the carbs are they plugged in properly...

 

So after reading your message I took of the tank and everything was hooked up the right way. I decided to put a new fuel filter on; did not have a chance to test drive it yet since it started to rain bad. I do have a used fuel pump coming from ebay. Hopefully one will work. The fuel pump cost me .99 cents and 15.00 for shipping. I'll let you know.:rock

 

Afriend of mine had this problem when he removed the fairing. Put the fairing back on and all was fine! Seems the fairing ensures the correct airflow to the airbox.

 

Not sure how much of a bog you get, but the '98's and '99's were known for this issue. There used to be a lot of debate on exhaust choice, needle placement and mains. What exhaust are you running? What have you done to the carbs?(what # jets) Are the carbs sync'd up?