I have seen the Vacaville Pena's pedigree charts.Though I am unable to recall the specific details you are looking for, I know they are out there somewhere.My 3x great grandmother was Amelia Pena, possibly a sister to your Prudencio Pena. If I come across the book with the Pena information I will be sure to come back and post it here for you.
For now I can provide you with information on your great great grandmother Rufina.Rufina is my great great great Aunt, you and I share a set of great great great great grandparents Sixto Antonio Berryessa and Maria Nicolasa Higuera.
Rufina was born in 1868 in Berryessa Valley, CA.She was the youngest of 11 children (6 boys 5 girls).Rufina's brother Julian is where my family descends. Julian also married a Pena - Emiliana (Amelia) Pena.