It sounds like what my bike does when it gets some bad fuel. Oh, charge the battery too.

 

Check for both intake and exhaust leaks, also timing problem. The bike mit need new spark plugs check them to see there condition.It mit running a bit lean. These are all the causes I can think of. The reason may be the exhaust leak, you say you need a new system.

 

Well several have hit the main parts. Go ahead and change you sparkplugs, clean, or replace your air intake to more allowing air flow model. Then check the back of the pipes for the o2 sensor or the sensor plug; check tightness, then check the tightness where the header pipe attaches to the twins. If it continues, then you might have a problem with a sticky valve, or timing