I am reading this thread and it is a hoot. Guy posts a complaint and you get defenders and aggressors and my favorite, those with no dog in the fight offering all sorts of "if you used me, this would not have happened." and "use me in the future and I guarantee this won't happen".
I will give you some facts on import, gained from my experience importing live dogs and cats through JFK as a pet shipper (agent) :
1. If is coming in through JFK it is going to cost more. It is NYC and the brokers and forwarders charge more. Fact of life. If you are not close to JFK, consider another USDA designated port of entry. I once had a guy carge $250 for about 10 keystrokes on a computer to clear the import. Seriously. But, the only way I could get it done.
2. I have used Fauna and Flora for my hunting trophies and they are excellent. Not cheap. Like most things in life, you get what you pay for. I'm not pimping for them as there are numerous others who clear, but I've not used them. If your trophies come in through JFK you are better off using a local agent. Why? Because occassionally, someone is going to have to go over to Customs or USDA and straighten it out. Trust me, it gets done a lot quicker in person, than on the phone or email. If you come in through Chicago, use a Chicago based agent. Sure the guy in NYC can handle it, but if there is a problem, he may have to call someone in Chicago to fix it. The freight side of JFK is lined with the offices and warehouses of customs brokers and forwarders.
3. Consider having someone clear for you and then you pick up the boxes at the airline and drive them to your taxidermist or home yourself. You save the ground freight from the airport - duh.
4. Clear them yourself. Gets done everyday.
5. Problems in Africa - it's Africa. What do you expect?
6. Think of it this way - you've made arrangements in Africa while you were there for dip and pack or taxid, then you leave. When it is ready to be shipped, you are several thousand miles away and emotionally and financially invested in the trophies. Think the guy is Africa might sense an opportunity to "pad the bill" so to speak.
7. The comments on co-mingling of trophies into the US are 100% correct. Customs used that line about record keeping - maybe. The real reason is security on any freight coming into the US. TSA wants one guys name and addy on the box so if something is not on the up and up, they know who to go to. That name and addy better be the same as on the bill(s) of lading and export paperwork.
8. Ocean works and it is cheaper. Slower, but cheaper. Makes sense. Right?
Use the above FWIW but I see this stuff day in and day out, through the busiest port of entry for air freight in the US.