I am not much of an Rmarkdown user. I have just played with it as I am used to Lyx + knitr but that YAML code looks excessive.
What is your desired output format? Currently it looks like you have calls into pdf_book, bs4_book, gitbook, & word_document2 .
BTW are you getting any error messages when you knit?
You might want to start with something basic such as :
bibliography: references.bib
csl: "apa.csl"
output:
bookdown::pdf_book:
citation_package: biblatex
template: templates/template.tex
```r
and see what happens.
Otherwise let's hope an expert arrives.