New regulations have been put in place for shipping into Malaysia. It seems before one could self-clear and only needed a carnet for a vehicle.
After 1.5 weeks of being in K.L. we finally sorted it and rode our bikes out of the port!
All foreign imports will need to engage with an agency in order for them to produce an "acceptance letter" for receipt of goods. This is the new change which discourages self-clearance. After quotes from a few companies in Malaysia, we used FM Global Logistics (sugu@fmgloballogistics.com) as they came out as half the price of the others and they were lovely people.
Before your vehicle arrives, you will need insurance and an ICP (circulation permit) (NOT road tax as we erroneously told by one agent- road tax is only applicable to people who want to register their vehicle in Malaysia and the minimum period is 6 months).
Insurance: we tried 3 companies in KL: UNI general Asia, Zurich and Kurnia. UNI general almost gave us insurance but it required so many emails back and forth that we lost patience. The others wouldn't insure foreign bikes over 500cc. In the end, we hired a car and drove to the border with Thailand and bought Zurich(!) insurance for $15 each (per month- for a 1200cc and 785cc).
ICP: JPJ sort this for you (dept. of transport). The headquarters are in Putrajaya. They're not really used to foreigners requesting temporary ICPs in KL yet (on the border it's not a problem, in fact they are next door to the insurers). You NEED an ICP to clear your vehicle through customs but JPJ need to see the vehicle to give a permanent ICP

a nice catch 22. Anyhow, they gave us a temporary one for a week under the promise we'd return to their office with the bikes once cleared. They can also arrange to come to the port to inspect bikes but I'm not sure how complicated that would be (we had to speak to three different officials before someone gave us ICPs after 3 hours of waiting).
With your insurance and ICP and carnet for vehicle your agent will help with the other documents you need for customs:
- registration as temporary importer
- import letter
-export letter (requires approximate date of departure and border you intend to cross)
- acceptance letter from agent.
- shipping invoice
- packing list (if applicable- didn't have one but we got away with it despite having all our camping gear and clothing shipped in the crate with the bikes)
- passport copy of every stamped page of your passport(!)
If you go first thing in the morning to customs with correct documents in hand (3 copies of all the letters) you can clear in a day and ride out that afternoon. be warned of the frequent public holidays (we arrived during chinese new year) and that Fridays no one works between 12-3pm.
Approximate costs (total paid was $400): this was divided by $180 to customs for two bikes cleared, $85 to shippers, $100 to agency and the rest for demurrage/warehouse/carpenter etc... Other agencies were asking $500 per vehicle on top of other fees. The storage fees are low in Port Klang thankfully, as our bikes were waiting there for 5 days before being cleared!
Hope this helps