If you can get a boat down there (paying 300 on united or getting a waveski onto american) it is really easy to fly with a boat with peru air (pay for excess weight, I think 1$ a kilo). I would recommend September as a great time to go.
I've flown to Lima with a boat. It usually depends on who you get at the counter no matter what the policy. You can always send stuff air freight/cargo often on your same flight. Just arrange ahead of time and be prepared to spend some time at your destination customs port of entry.
Always have a plan B ready if you get denied at the airport check in counter!
I found that traveling by bus in Peru with kayak was the real challenge. Be ready to "tip" or financially encourage the bus bag handlers as they can be difficult.
Most likely you can sell the boat and other stuff for a good price so your return you wouldn't have any issues. Recommended.
By mid october stuff around santa terisa is most likely going to be low/rain dependent, when we were there we this year in mid october we got a rain pump and got the santa terisa at low flow, the sacsada, the urabamba at huge flow and the vilcabamba at good flows. Locals made it sound like the area is much better in july/august for paddling in that area. But just my 2 cents
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