Yes this is very familiar we had to teach all of this individually. eg wording a question differently would be like teaching the skill for the first time. Over time DS expressive language has become more flexible and less rote, and then his receptive understanding improved. He's 6 and this has really only happened in the last year
He often found matching written words easier than doing it orally - eg matching the words on, in, under to situations / pictures and then once he had grasped it this way he could move on to oral questions / answers. You can do it receptively too eg show me 'in the box' 'on the box' etc Sometimes learning the new skill (preposition) plus processing the verbal information plus processing the verbal response was too hard all at once. Often we only had to use written prompts a few times.
DS would always rote learn his programmes so we had to be very careful to very them and mix them up so he really learnt the skill and not just the programme. So making sure he could discriminate between programmes / instructions and not just taking the cue from the materials.
He rote learns easily and has an amazing memory. For eg he learnt about 8 songs word perfect for school nativity despite having no understanding whatsoever what he was singing about. It must be like me rote learning a song in Japanese he just remembers a string of information exactly as he hears it.
An ipad is great - I mean he still rote learns things from apps, but the sheer number of examples you can get through by letting him play on an app really helps
He is now 6 and is moving on to having to figure things out eg novel problems, pieces missing, things in wrong place etc. He finds this incredibly hard. Also to generating own ideas eg for drawing. We had to start with giving him options until he built up a 'bank' of ideas to pick from. He really couldn't do anything that was not rote learnt to start with but its coming.
We've also done a lot of work on observing others eg other children as a skill to help him -so in school if he's not sure what to do he will look and copy another child. However he's now got so good at this he now often under listens and copies even when he shouldn't!
Wh questions came a long time later and we are still just part way into this.
You might have to give him the start of the sentence as a prompt eg 'what is it' 'its a...' to help. Then fade this out.
The fact he has a great memory will help. DS is so like this and slowly but surely he is making progress.
Have you ever read anything by Temple Grandin. She very much describes learning things one by one and filing each example as a 'picture' in a mental filing cabinet and she will pick out a previous picture to complete a task given.She describes learning very much as a cumulative thing - learning things layer by layer until eventually it comes together. She is regarded as very high functioning as an adult so I find it very reassuring she was like this at a similar age. For example she says she did not realise all dogs were dogs - to her each was a completely new animal and she had lots of 'dog pictures' filed away and eventually she made the connection they all belonged in a group called 'dogs'.
The Autism Partnership book 'A work in progress' is very good at setting out ABA programmes for all of these skills and helps with the order to do them in.