I have never actually speed tested this machine until recently. I was always satisfied with how fast it passed 100. But after the sprocket changes I decided to take it out onto the newest, smoothest road rural Illinois has to offer and see the results of 18/38. Again, I was surprised that it seems to go right up to 125 like its going to go right thruough and it's like it hits terminal velocity. Eventually will try the old gearing and see if the powerband is better used with those.
Don't bother changing your sprockets, just keep it in 4th gear and see how fast it goes. On your 18/38 gearing, with a standard 150/80x16 back tyre, you would be hitting 150 mph if it would rev out to 9500 rpm (redline) in 4th and should be flying through 135 mph at 8500 rpm
That's not too far off what you'd be getting (156 mph) in top gear if you went back to standard 17/40 gearing at 9500 rpm.
If it won't go much over 125mph in 4th and you're not going uphill, or into a strong headwind, then I'd say you have another problem - if nothing is dragging (brakes, which is unlikely or you'd probably have noticed that) then your engine could be down on power for any number of possible reasons, including carbs, ignition, low compression etc, but there would be other signs with some of those issues and you haven't mentioned any of those yet.
One "out there" thought I had was, where did your bike come from? - is it an official Yamaha import?, or could it possibly originally have been from another market?. Some European spec bikes were limited in power and Japanese home market models would have been restricted to around 118mph.
Either way, checking out a 4th gear run and then maybe doing a compression test might give you something further to look into.
Best of luck and please keep us informed on your findings.