My pdf reader is mupdf. It works and is on my PATH. My rifle.conf is (relevant part):
#-------------------------------------------
# Documents
#-------------------------------------------
ext pdf, has mupdf, X, flag f = mupdf -- "$@"
ext pdf, has zathura, X, flag f = zathura -- "$@"
ext pdf, has llpp, X, flag f = llpp "$@"
ext pdf, has apvlv, X, flag f = apvlv -- "$@"
ext pdf, has xpdf, X, flag f = xpdf -- "$@"
ext pdf, has evince, X, flag f = evince -- "$@"
ext pdf, has okular, X, flag f = okular -- "$@"
ext pdf, has epdfview, X, flag f = epdfview -- "$@
I ran --copy-config=all and made sure the config file in my home dir was configured as above. I also used locate to search for any other config files and configured them as aforementioned too. I tried running ranger with -d (debug) but it did not provide any useful info for debugging this issue. Ranger used to work with zathura IIRC, and it works with other document types.