So, I spent some time on this and found out a better workaround without having to use terminal. By using the "do shell script" function, I can make the applescript a lot more simple :
do shell script "cd /Users/Username/folder; /System/Library/Automator/Combine\\ PDF\\ Pages.action/Contents/Resources/join.py -o final.pdf cover.pdf content.pdf"
This way we avoid Terminal from having to open/close in the background. I created a test calculation field to find the correct syntax, which turns out to be :
"do shell script " & "\"cd /Users/jaredhagan/desktop; /System/Library/Automator/Combine\\\ PDF\\\ Pages.action/Contents/Resources/join.py -o final.pdf cover.pdf content.pdf\""
Filemaker opens an merges two PDF's, cover.pdf abd content.pdf, and the product is final.pdf.
Hope this helps,