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Does Amazon charge an FBA fee for every unit sold or per total shipment to their warehouse?

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Change the "or" in your question to "and", and the answer will be YES.

There is a charge to ship your product to the Amazon warehouse; this covers nothing more than the shipping charge, whether small parcel service with UPS, or LTL/FTL. Amazon will receive your shipment, unpack it and check it in, then start charging you storage fees.

Then when you sell an item, Amazon will charge what you see listed as "FBA Fee" to cover the cost of picking/pulling your item from its place in the warehouse, packing it in a box, and delivering it to the customer. Note that FBA fees are ON TOP of the regular selling fees, which vary by category but are typically 15% of the total amount (plus $1.80 if you are selling media, plus $.99 if you are on the individual plan).

It sounds as if your math skills are fine, but you are now realizing that you did not have all of the numbers to plug into the calculation. At least you are figuring it out now, and not (like some) only after losing many thousands of dollars.

Note that on top of all the other fees associated with FBA, there is also a fee charged to have your items returned to you, or removed from inventory. Selling what is left at a small loss might still be better than recalling your inventory, especially if you lack another outlet to sell it at a true profit.