You can say 'I don't understand what you said/ are saying.' or 'I didn't understand what you said' (if you are talking about a present situation. You can say 'I didn't understand what you had said to John before we left the party yesterday' ( the action in the past perfect (had said) happened before the action of leaving and understanding) or 'I didn't understand what you said to John before we left the party yesterday'. (You can also use past simple for all actions because before tells us which action happened first) If you use past perfect you have to put the verbs in context with time expressions or adverbs so we know when the situation was.

They're both wrong. I don't understand what you're saying. I couldn't understand what you were saying. I didn't understand what he was saying. I never understood what you said. These are the correct forms.

I didn't understand what you have JUST said. or I didn't understand what you said. 'had been said' doesn't make much sense ,it is a passive form ,that doesn't suit in this context. Using the past participle as well doesn't is not appropriate in such a sentence.

The proceeding work with the given forms: I didn't know what he was writing - Я не знал, что (именно) он пишет. I didn't know when he would call me up - Я не знал, когда он позвонит мне When he came, we had been waiting for him for a hour - Когда он пришел, мы уже час ждали его. The firewood had been built into three piles - Дрова были сложены в три штабеля After all that had been said you may continue doing exercises.