The first problem sounds like you just needed a new battery and drive the bike at to low of an RPM. If I run below 3500RPM it lugs the motor. Check your voltage out put to be sure on the battery thing.
#2 when my bike is cold it also does a nock, nock, nock kind of noise it goes away when warm or if I raise the idle a little.
From your description it may be different things but I would try turning up the idle to 1300 to see if the gets rid of the noise.
I have been told by others with more knowledge of these thing that the nock,nock,nock is the clutch and is normal. I don't know if you have the same but worth a try.
good luck