What he is experiencing is certainly a symptom of bad fuel. This is especially true with blended fuel (E-10). Phase separation occurs where the fuel separates from the alcohol. Under these conditions alcohol attracts water that may pass through the system resulting in a misfire or hesitation. The engine then may run fine as non contaminated fuel is being fed through the system. It may be other problems you have but it may also be fuel.

If you are not running a 10 Micron filter I would install one.