Wow, My Roadie absolutely HATES BEING LUGGED. She'll protest if I even try to use 5th gear at speeds lower than 80km/h (50mph) ....I don't rev the crap out of it beforr upshifting either....
Those goofy recommended upshift points in the Yamaha owners manual are way outa whack!
When you get an engine bucking at low RPM's it means it's running too slow under load to be happy.
One reason for the bucking is that the air and fuel don't mix properly and therefore don't burn properly. The other reason for bucking is spark timing, cam/valve timing and "flame-speed" of combustion. Severe lugging is very hard on con-rod bearings, rings. pistons, etc.
An air cooled motor can't cool or lubricate itself effectively while in ligging conditions under load.
Lugging also can lead to excessive carbon deposits due to improper combustion and expulsion of combustion byproducts.

Any engine engine will only perform within a limited RPM range according to the way all is set up.
This is why those high-RPM racing engines in cars will not idle properly at 700 RPM (they buck, and surge at idle because the cam-grind and spark timing at all set to run at 3,000 to 6,000 RPM's ideally.

Just my two-cents worth on the subject. Hay Bay Woody has a good point on broadening the useable torque-band of the engine.
I recurved the injection timing advance on my '93 Cummins diesel so it will now pull like crazy from 1400 to 2900 RPM and still sound happy doing it at 711 ft/lbs peak torque.
Stock setup was a VERY NARROW TORQUE BAND with 400 ft/lbs torque only betweem 1700 to 1900 RPM. They did this to meet emission requirements. At 2,000 RPM it was out of steam and not sounding happy (117km/h) This narrow stock torque-band was frustrating with only a 5 spped tranny with large split beteween gear ratios on upshifting, 3rd was screaming and 4th was lugging when pulling 16,000 lbs. upshifting on steeper hills. I probably make a little more greenhouse gas now, but it is a way more driveable towing rig now!
It's all in the details of how you set it up.
...Now it pulls like a champ all the way till the governor cuts in at 2950 RPM. (172 km/h)