Hey thanks for the detailed response. Very much appreciated!
Our plans have slightly changed due to new limitations on when we can depart YVR (missus' project commitments). Originally, we were hoping to have more time pre-cruise. Instead, now we're planning to head back to Malaysia after we end our cruise in HK so we have a little more flexibility in terms of a visit of Malaysia even though that means kind of doubling back a bit.
The timing suggested for Penang and Malacca seems to align with what we're thinking as well as a short visit to KL. The info about travel between cities/towns was helpful. With the additional time we now have, we might be more inclined to try to make some quick visits/side trips to towns in between our main stops.
Also, not sure now if we'll fly home from SIN or KUL now depending on what flight options/fares we find.