Yes, "ça fait" can become "ça faisait" if you want to speak about the past.
The part "que j'avais commencé à prendre les commandes” sounds a little bit weird.
Maybe use "ça ne faisait que trois jours que j'avais pris les commandes" because in french we understand that you started 3 days ago.
I just want to add one thing : "ça fait" and family ("ça fera", "ça faisait"..) are speaking language. Do not write it down. Instead you should use the 'full' word for "ça" wich is "cela".
Like this sentence : "ça fait trois jours que je marche" becomes "cela fait trois jours que je marche".
However it doesn't work everytime if you want to use "cela" instead of "ça". For instance, "ça va?" (How are you?) can't be "cela va?" because if you uppgrade the "ça" to "cela" you also have to upgrade the "va" to "va-t-il" and add a "Comment". So "ça va?" becomes "Comment cela va-t-il?"