Answer from cs61c-al (Phillip Chin 16156822) for Question 2
These signals are coming from the EX/MEM, ID/EX and the MEM/WB. Essentially these are futher down in the cycle and the new values are being written into. Depending on what stage you are in, determines which signal is written and sent to the register. So if it was a write then a read, the read would be at the EX/MEM stage since there's a one cycle delay.