Are these expressions used in spoken English?
It is time for him to take the bus/to have taken the bus.
It was time for him to have taken the bus.
“It is time for him/her/me/you/etc. to (do something)” is a common expression in spoken English. Remember that in speech “it is” is almost always contracted to “it’s”, unless “is” is being emphasised. “It’s time for him to take the bus” is good English, but this specific example is perhaps not especially likely to be said in real life. I guess “It’s time for him to get the bus” is more likely.
“It is time for him to have taken the bus” doesn’t sound right.
“It was time for him to have taken the bus” doesn’t sound very natural either. If you want to put the expression into the past you would normally say “It was time for him to take the bus”.