The jerkiness of shifting may be caused by rider error, old oil, wrongly adjusted shift pawl, but usually its your chain. Make sure you chain is within adjustment and is lubed correctly.
The bogginess of your motor could be a million things. I'd check your air filter and even if it looks clean, clean it, and then you can further diagnose your problems. It could be bad gas, a clogged jet, a clogged vent, etc.