I am very confused right now. I had a period for June, but it was the last couple of days of June and it ended July 2nd. I never got a period for July and then I got one 3 weeks into August. I took 2 HPTs and both were not very clear, it looked positive and negative (very faint color). Than I got my period, it was really light for the first two days and than the 3rd day I was bleeding really heavy.
I have back, neck, stomach problems and my breast are so sore/tender that I can't touch them without hurting.
What does this all mean?

These can all be symptoms from you having your period. You should probably just go visit your doctor and he will get it all straightened out for you! :)