Bought the ticket already?Maybe it is more natural to arrange like below:
Hk->kl->malaka->jb-> SG -> Hk.
KLIA is far away from town so troublesome to travelvia klia.
U may try the bus but not that enjoyable rwt by hotel u stay.
Not sure how old ur kid is.U may try to take train which can give u another feeling.But be reminded to check the train schedule and have to take the fast train.Also the ac is very strong in the train so need to bring jacket for sure.
Here can give u an idea on train travel in Malay.
http://www.seat61.com/Malaysia.htm
In kl, u may go to bird park which is aged but can let u have a closer look on the bird (really close).