[Timber]

Fixed it. Now running perfectly for all of opening the ebook-viewer app, using it to open a specific file by dragging and dropping onto i and associating with an ebook file extension to open a book by double clicking on it or right clicking on it.

Thanks to loximuthal for pointing me in the right direction

In case anyone else wants to do this, here's what I did

Open Automator and choose to make a .App
Set it to take passed parameters as arguments
Choose Run shell script from the actions (middle column) and drag to the script (right column)
code for the shell script that worked for me

if [ "$1" != "" ]; then
/Applications/calibre.app/Contents/MacOS/ebook-viewer "$1"
else
/Applications/calibre.app/Contents/MacOS/ebook-viewer
fi