We would like to use a third tough box.
From our reading the rules, we feel it is legal if we buy all the pieces of a tough box separately, in order to not exceed the $40/item limit. Is this true? 
Answer:
The tough Box exceeds the $ limitations.
Attempts to circumvent the rules to a teams advantage is not in the spirit of the competition. Following your logic the $50 limit would be meaningless for almost everything.
The Tough Box is considered an off the shelf assembly in excess of the limitation.
Final answer is NO you will be required to remove it if you use more than 2.