Well, we're 1st cousins, 8 times removed via Epifanio Marques & Maria Estefana Martin de Marques, Baca, Grijalva y Gorduna, whom we share as direct ancestors. We're also half-relations equally removed as above via Juan Manuel Baca/Vaca (of Vacaville fame). He is one of your 3rd-great grandfathers and a step-3rd-great grandfather for me (as well as for you). You see, Estefana Martin, mentioned above, married J.Manuel Baca/Vaca after Epifanio Marques died. So it's complicated. We're probably related in other ways as well because nearly everyone with an ancestor from New Mexico in the 19th century or earlier seems related to nearly everyone else there.
As for how else your sister may be related to her husband, Michael Vincent Baca; I'd need to know a lot more (e.g. his parents and grandparents) before I could even hazard a guess as to how far back they're related. Five generations back is certainly possible; but it could be as many as eleven or twelve. "Baca" is just about the most common surname among Hispanos (the hispanic people of New Mexico and southern Colorado) after "Martin"/"Martinez".
However, your New Mexican ancestors most certainly did NOT come directly from Spain! Your earliest Baca ancestor, Cristobal Baca (who is also the earliest Baca ancestor for all New Mexico Bacas), arrived in New Mexico from Mexico City about 1600. He and/or his children were likely present at the founding of Santa Fe, which is celebrating its 400th anniversary this year!
I have some questions for you, too. But they are about much more recent descendants; so I'll try emailing them to you directly.
--Alex. King