way tooooo much time in transit it seems to me..

I agree with Bob, cut the number of your destinations and you'll have more time to enjoy your time in SE Asia.

For instance, while Melakka is interesting, it interesting, it doesn't hold a candle to Penang. I'd cut Melakka and maybe even KL (not my favorite city) and fly from Singapore to Penang, staying in the Georgetown area.

Khao Sok, of course, is nothing like Borneo. We were in Sabah and Sarawak in November, and while we did rain in Kota Kinabalu, we didn't get much of any rain in the jungle. If Borneo is what you really want, go there. Don't let the rain deter you.

I agree with Kathy you can cut KL but to me Borneo is a must. We were also there in the rainy season but nothing stopped us from doing whatever we wanted to do, on the contrary the rain is a relief with the hot and humid days. We did a homestay in the Kuching Sarawalk river area which was one of the the highlights of our Malaysia Thailand trip, the first being Sipadan for the diving.

i have been to both and i would cut them

I have been to all the places on your itinerary, some several times. My least favourite places in your itinerary are Singapore which, personally I find a soulless place although it does have some great hotels and would just use it as transit point, staying for only a day or two to get over jet lag. I would avoid Phuket completely unless you are just looking for a international style hotel. It is just too overdeveloped these days. There are much nicer beach places on the Andaman coast which will provide a better, more "authentic" Thai experience. There are also some great beach resorts in Malaysia. Langkawi is just south of Phuket, has some amazing hotels and is a lot quieter than Phuket. You can even get there by boat from Penang as we did. It only takes a few hours and is a really nice trip.

Melaka and Penang are both nice destinations for a couple of days apiece, particularly if you are foodies as both places have some of the best food in Asia, have interesting centres for sightseeing but lack any decent beaches. KL is not a favourite place on this forum but I love it. Loads to see, do and eat you just have to work a bit harder to seek out the best bits! Melaka could always be done in a day trip from KL? It takes about 2 hours by bus, a little less by train.

Borneo is worth reconsidering. It rains all year in Borneo but rarely all day. It usually happens in very heavy downfalls followed by sunshine and so should not affect your enjoyment too much. If you are up for a challenge, climb Mt Kinabalu, if not head for the rainforest both are spectacular .