Q: How can we solve this amicably? We want to pay the remaining balance, but for the proper amount.
A: The only way to solve this amicably is for you and the company to reach some sort of settlement or agreement as to the charges, and for you to pay those charges in return for your items. Accordingly, if I were you, I would try to open lines of communication with them, explain that you believe that the bill is inflated, and ask them how they arrived at the total amount. It's possible if you go over the detailed bill with them, that either they or you will realize a mistake, and all parties can come to an agreement as to the amount owed. If that does not happen, then you have no choice but to file a lawsuit against the company.
Q: Should we file a police report for stolen goods?
A: No, that will do you no good. The company didn't steal the items; you gave the items to the company to hold for you. To clarify, theft occurs when a person takes another person's property unlawfully. The company didn't take your items unlawfully because you gave them to the company. Accordingly, this is not a criminal case; rather, it's a civil dispute.
Does that answer your question? Please let me know if you need clarification, as I am happy to continue helping you until you are satisfied. Also, please remember to provide a positive rating via the stars (and note that your positive rating is the only way that I'll get credit for helping you, so it is much appreciated!). Thank you. :)