The clock period has to be slow enough so that all of the signals can propagate through the system well before the next clock cycle starts.
Part of your problem might be hinted at here:
arthan1461 wrote
1st Clock Phase (START)
@3 binary representation (0000000000000011) enters the in-pin of A Register
Since @3 is an A-Instruction, A register will be loaded with the input but will yield the output during the start of the next clock phase
The A register (like all of the memory elements) loads the data at its input on the rising clock edge and, once loaded, it is immediately transferred (subject to propagation delay through the device) to the output.
So during the 1st clock period the value 3 is applied to the input of the A-register, but it is NOT loaded at this time because that requires a rising clock edge. Similarly, the instruction decode logic asserts the Load input on the A-register, but nothing happens yet.
On the next rising clock edge the value at the input gets loaded and appears almost instantly at the output. At the same time, the same clock edge is also advancing the program counter which is then changing the instruction address so that the next instruction becomes available, which will make the values at the inputs of the A-register change (potentially). As long as those values were held valid long enough for the load operation to complete, we don't care. This is why we need the propagation delay through the sequential elements to be longer than the hold time.
1st Clock Phase (END) == 2nd Clock Phase (START)
1. A-Instruction goes out of the A-Register
2. addressM pin will be loaded with the A-Instruction
3. C-Instruction (M=M+1 == 1111110111001000) enters A-Register in-pin
(from my understanding these three processes above happen simultaneously)
The C-instruction includes the control signal that configures the Mux that's ahead of the A-register to change so that the input to the A-register comes from the data ram and NOT the instruction.
See if you can use this new knowledge to work out the rest of it. If you still have problems, post an updated description as you currently see it and we'll go from there.