1. Tribes people, actually called Kothoga, fed Whitney the soup made from the virus infected leaves (made it more potent). They saw him as an enemy only he didn't know that.
2. He was looking for the crate containing the leaves, he must have discovered something about their true nature and that he needed them to survive.
3. It was headed to Chicago Museum (NYC in book), sent by Whitney himself. Only when he sent it, he wasn't aware of what he had. That's why he rushed over to try and stop the shipment. Maybe he didn't want to go back. It's a bit vague in movie, but I'm guessing he must have realized the potential danger of what was happening. Although this was not the case in the book, he didn't connect all the dots. And yes, it was mistakenly left behind and sent via air freight.
4. During the the sail from Brazil to Chicago (I'm not sure if there is an actual shipping route to that port from Brazil), Whitney began to mutate into the Mbwun (actual name for monster). Likely he jumped ship first opportunity he could get when it was safe to do so unseen. There were underground service tunnels right at the port which he took all the way to the museum, likely it was a large network of tunnels. The monster had keen sense of smell so finding his way around was not impossible. He didn't arrive in those boxes as characters thought.
Hope this helps.
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