Something you my wish to try.
Buy some brand new plugs and take them with you on the ride, along with a spark plug wrench.
With the engine all warmed up Find the area of road where you believe the engine is weak.
Put in the clean plugs and operate the engine in "weak mode" for as long a duration in time as you can.
Hit the kill switch, pull in the clutch, and coast to a stop. Put the old plugs back in and then take some pictures of the spark plug white insulators so we can see the strap, the as much of the porcelain as possible. (will tell us if the mixture is correct)
Also, find and measure off 1/4 mile. From standing start, time how fast you can reach the 1/4 mile mark and what speed you have on the clock when crossing the line. (Will tell us if the bike is performing correctly)
If you want to pass a vehicle at 60MPH and really want to scoot, expect to downshift at least 2 gears (or even three) and that should get you around whatever is blocking your path pretty quickly. If you have plenty of space and patience, it should pick up speed even in top gear.
With the smaller displacements, the transmission is half as important as the twist grip and work together as needed. The rider is more responsible for anticipating what gear is needed before the acceleration is actually needed.
I didn't have my 400 very long, as I didn't like how "skittish" it felt overall (compared to my Cb550s). But, I don't recall any issues on the freeways or long hills. Obviously grade matters. But, then I'm used to just having the trans is whatever gear is necessary to get the job done or keep the engine in the power band.
If all you've ever used for acceleration is the twist grip, I can't imagine you ever being happy with using your left foot as much as your right hand.
Cheers,