My mistakes in using tenses

• I'm sorry I didn't answer the phone earlier, but I was painting/had been painting the ceiling in my bedroom. 
• By the age of three, Mozart had learned/learnt to play several pieces of music.
  The Past Perfect expresses the idea that something occurred before another action in the past. It can also show that something happened before a specific time in the past. 
• Paul has stayed/has been staying in all day today, so now he feels like going out. 
• I thought I went/had gone into the wrong garden. 
• I haven't been to Siberia before. AND I have never been to Siberia. 
• Why on earth didn't you tell/haven't you told me adout that loose floorboard?(It is no longer in the present because of the next sentence) I tripped/have tripped over it just now and hurt myself. (Two actions one by one and there is a certain time) 
• David has called/has been calling me up in the middle of the night and told/telling me his troubles. (Repeated action) 
• Harry has left home rather suddenly and we haven't heard from him since. (It was in the past, not recently)