Does anyone have any advice or recommendations of the best way to ship a 5.4 m long sea kayak to Nakhonsawan from Phuket?

If I were you I'd ask around at the local bus station, I'm sure you'll find a bus driver going to central Thailand who will be willing to strap it to the top of his bus for a small fee. I would suggest you either supervise the strapping down or do it yourself though!

Perhaps Thai Post can do it as they have a lot of experience with posting odd shaped items.

I know that they ship motorcycles for a start.