I think the sign of the tension force that you obtain for the cord between two blocks will depend on which equation you use to solve for it. Regardless, the tension everywhere in the cord between two blocks is equal in magnitude (meaning disregarding the sign).
This is incorrect. In writing ##T_{CtoB} = m_Ca##, you're saying that tension is the only force acting on block C. The acceleration a is the net acceleration of each of the blocks, period. It is the result of ALL forces involved ,not just the tension and not just gravity, all of them.