1) Nah, she'll marry OTL Manuel I of Portugal.1. I did that with the idea that Richard thinks it will stop anyone from gathering around them to try and overthrow him.
2. She is a good fit for a Duke of Gloucester and the second son and could offer an appropriate dowry.
3. That was a mistake thanks for catching that! Also what does Afonso of Portugal living have to do with anything?
2) I think he'll marry an heiress, personally, or atleast a higher ranked french bride. Maybe Margaret of Angouleme (see below)
3) Joanna's kids would higher in succession than Manuel, so Richard's eldest son by her is going to be king of Portugal in the event of Afonso dying. So he can get a high match than Margaret.