Thanks for all the great responses. Sorry I didn't check in sooner but I didn't get the notification of postings for some reason.
To address the questions:
1. Putting it in a box is definitely easier and safer, there is no doubt about this. But it is dramatically more expensive - the two biggies being import tax in Panama and the container insurance. The other costs are more or less the same. So I'd like to avoid this if possible.
2. Staying on the Atlantic coast makes sense but it is a long way and involves more border crossings. But potentially safer. I'll play with the flight plan and see.
3. I'm actually working with SeaMax Brazil's owner of the company / designer of the airplane. He's a great guy and has been super helpful. He's flown the aircraft to some pretty wild places before so he is confident that this is a doable trip.
4. I've found out another wrinkle: if I keep the aircraft registered in Brazil, I must have a Brazilian licensed pilot fly it. My licenses are not valid to act as PIC.
5. I totally agree about range being the biggest issue. I contacted Turtle-Pac and they make some very cost-effective solutions, one that would go behind the seats for 2 more hours' flying time and another which could replace the copilot seat and add a lot more. The latter would mean that I couldn't go on the trip but it might make it safer for the ferry pilot.
Thanks again for all the great feedback and please let me know if anyone thinks of any of any other things. I'll keep monitoring and replying to this forum.
Oh, and if anyone is a Brazilian-licensed ferry pilot with a float endorsement who doesn't show up in the search of PPRuNe for "bad ferry experience", please get in contact with me - I have a potentially very fun job for you!