I actually thought about doing the same thing a few months back but gave up simply because it took too much time. Along the way from Kuala Lumpur, stay at the Hilton KL which costs 30k points per night, or Doubletree KL (even better deal 10k HH points per night).

3 nights in KL @ Doubletree KL = 30k points ONLY. I assume you're Diamond with that many points. You will get suite upgrade and lounge access which is great.

Take a train from KL sentral to Hat Yai. It's going to take a long time (more than 10 hours) to reach Hat Yai, so I think it's better to pay up and get the best cabin available. You'll reach Hat Yai next day morning at around 10.40am IIRC.

Spend the night in Hat Yai. I recommend the TuneHotels. Very cheap. Of course, if you could get some sleep on the train, then you'd best forget about spending the night in Hat Yai... I don't find it an interesting place.

From hat yai, take a train to Surat Thani, and then take a combination of bus and ferry to Koh Samui, if you feel like it. The Conrad costs 95k points per night though.

If Koh samui doesn't float your boat, you can take a train to Phuket. A couple of Hilton properties there.

From Phuket/Surat Thani, you can journey up north and stay a few nights at Hua Hin, then Bangkok. Should use up at least half your Hhonors points very easily.

Too bad, you can't buy your Thai Railway train tickets online now... would make your trip-planning much easier!