Backpacking Route Planner
Malaysia

I've set up two itineraries: One for the Eastern coast of Malay Peninsula and one for the Western coast of Malay Peninsula.

The reason is the monsoon weather which affects these two parts of the country differently.

It all depends on when you're going. The Eastern coast of Malaysia is affected by the heavy monsoon period between November and March.

While the west coast has its monsoon period between May to September. In other words, if you're planning on sunbathing on Pulau Langkawi, Penang or Pangkor Island during this period, you'll probably get disappointed.

Malaysia itinerary -- Eastern Coast + Borneo:

Time: 3,5 weeks

Kuala Lumpur Kota Kinabalu (Borneo) Semporna (Borneo)
Back to Kuala Lumpur Kuala Besut (possible overnight)
Perhentian Islands Back to KL

From KL --> take a flight to KK in Borneo, or take a flight straight to Tawau if you just want to go diving in Semporna (Sipadan Islands)
Depending on when you leave KL for Perhentian, it's possible you have to spend the night in Kuala Besut.
One option is to take the night bus from KL, arrive early in Kuala Besut around 5 am, then take the earliest boat (7.30 am). Then you won't need to spend the night in this nothing-to-do town, but you do have to try to keep your eyes open for a couple of hours.
Another option is to take the bus from KL at 9.30 am (from Putra Bus Station) and hope that the bus catches the last boat at 5.30 pm.
In the high season, buses stop Kuala Besut from KL if there are enough people (which in many cases there are), or else the bus will drop you off at Jerteh.
If it drops you off at Jerteh, take a taxi (15 RM -- 15 minutes) to the jetty in Kuala Besut.

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Malaysia itineary -- Western Coast

If crossing the border from Southern Thailand and continuing to Singapore...

Time:

From border crossing Kuala Perlis Pulau Langkawi
Penang (from Butterworth) Lumut (stop-over to Pangkor Island) Pangkor Island Back to Lumut (stopover to Ipoh)
Ipoh (stopover to Cameron Highlands)
Cameron Highlands (Tanah Rata) Kuala Lumpur Melaka
Johor Bahru Singapore

If you've just come from the Ko Tarutao National Park in Thailand (like Koh Lipe), you can just take the boat directly to Pulau Langkawi instead of traveling back to the mainland.
As far as I know and researched, there are no direct buses from Lumut to Cameron Highlands (Tanah Rata). You have to take the bus (1,5 hours) to Ipoh. There should be a direct bus from Ipoh to Tanah Rata which should take maximum 2 hours depending on the weather and the type of bus you're riding.
From Johor Bahru to Singapore: 1 hour bus ride and it leaves every 30 minutes
You can also travel directly from Penang to Medan on Sumatra in Indonesia. It should take you 4 hours. The ferry from Langkawi to Penang takes 2 hours.