I'm not a teacher but I'll try to answer the questions. I hope moderators would correct my answers if they are wrong.
[1] I wish I had learnt Spanish at school. ---> The truth is you did not learn Spanish at school.
[2] I wish I learnt Spanish at school. ---> The truth is you are not learning Spanish at school.
[3a] I wish I understood what they said. ---> The truth is you do not understand what they said in the past.
[3b] I wish I understood what they
are saying. ---> The truth is you do not understand what they are now saying.
[4a] She wishes we could come. ---> She wants you to come but you can't.
[4b] She wishes us to come ---> She wants you to come. Neutral about whether you can or not.
[5] I wished he came. ---> You wanted him to come at a past time but the truth is he did not come then.
![Devil [6]](/emoticons/emotion-14.gif)
It was high time for us to go.
paco