I have a 2008 R1, my first so I don't know if this is just normal for the R1 or not! I only have 300 miles on it right now. the engine revs good in neutral and above 4000rpm`s, but getting to 4000rpm`s it feels almost like its bogging down. I want to say its almost like a low rumbling hard vibration from the engine with slow acceleration. becomes more pronounced with harder acceleration.
I have a 00 R1 that has the same characteristics as you describe. I have always thought that it was a normal characteristic of the bike, but I have read that the earlier R1's were known for having more usable torque down lower in the rev range compared to the newer R1's, so I wasn't 100% sure if this characteristic was normal or not.
If I'm at say, 2,500-3,500 rev's, in say 2nd gear, the bike will run great with slow, minimal, progressive throttle input. On the other hand, If I apply too much throttle, I experience a vibration. Increasing the throttle at this engine speed (say 2,500 revs all the way as high as 4,000 revs) does not have an effect on acceleration, meaning it does not accelerate more, it just causes the vibration. Just like you said it becomes (the vibration) more pronounced with harder acceleration (more throttle/too much input).
AT 4,000 revs, I can start to apply more throttle, and the bike will run well, but I still can't crack the throttle all the way open without experiencing even a slight vibration till I am at least 4,500-5,000 revs.
If I am cruising on the highway in 4th or 5th gear, my bike will run very well at in between 3,700-4,200, as long as I don;'t apply TOO MUCH THROTTLE. In terms of cruising, I would say that my bike runs the best in between 4,700-5,000 revs.
After reading your post, I am convinced that the vibration with heavy throttle input at in between 3-4k rpm's is a normal charicteristic of the bike. I just thought that being it is a 1,000 cc machine, and the fact that it is one of the earlier models (the earlier models being known for having more low rpm grunt) it would have more grunt in between 3,500-4,500 revs.
My plan, when I have more time/money, is to have the carb's re-sync'd, and have the carb's re-jetted and see if that makes a difference. Ultimately, it definitely needs a gear change. I don't do a lot of high speed, (unless I'm in a straight line) so I think it would be a better bike for me to gear it lower.
I do a lot of riding on a real tight, twisty, steep mountain where I live. The road is so tight, that sometimes 2nd gear is too tall, but 1st gear would put me unnecessarily close to 6k revs. Like I said, I wish it had more usable torque down low, but the bike, ultimately needs to be geared lower.
As far as highway/freeway is concerned, I don't have one complaint. At 50-55 plus mph, it's a great bike, it's just on roads like the ''Oakville Grade'' that it is not well suited for.
A gear change will make my bike potentially a lot quicker from 0-100, (
) as well as becoming more suited to tight ass twisty, steep mountainous roads.