This border crossing is quite remote, and although it's busy with Thai and Malay traffic, relatively few foreigners cross here. Especially using their own transport.
Thailand (Time to process: 1 hour)
The customs department is first. If you approach the border from the town, you will come to a cross roads with the border to the left, and the customs offices opposite. Go into the customs compound and park. The kiosk for the central lane dealt with my paperwork.
For my transit, after vainly hoping that I'd just vapourise along with my headache-inducing carnet documentation, the Thai customs authorities woke a guy whom they either disliked most, or thought knew about Carnets. Then they stood back and watched him have an anxiety attack. Eventually, after disappearing for a month, he returned, revitalised and full of confidence to complete my documentation.
Even though my Carnet had expired, which for exporting purposes, isn't usually a problem, he noticed, and understood that this wasn't an issue.
When finished with the customs, DO NOT GO WITH YOUR VEHICLE TO THE IMMIGRATION OFFICES: there are parking spaces marked out for three motorbikes, which will already be occupied by thirty five scooters. Walk to the border on foot, have your passport stamped. Then return to your motor and drive it through the border.
Malaysia (Time to process: 1 hour)
Before we start, just accept this. When you've finished reading, don't ask any questions, or look for any logic.
Just over the border, there are some large blue customs inspection sheds on your LHS for taking HGVs to pieces. In front of you are the normal vehicle lanes, with the lane for trucks on their left. I was directed into the truck lane. There are no pull-in bays: when you are in the lane, there is no way around you. So, when you the guy in the kiosk tells you that you need to fill in a form which you must collect from an office 50m away, you become extremely popular with the occupants of the truck behind you.
To avoid this situation, pull up just after the large blue HGV dismantling/inspection sheds, go into the office to the left of the vehicle lanes and collect your blank paperwork. Then get back into your vehicle and try to re-enter the flow of traffic. Now, Thai drivers are generally skilled, careful and spacially aware of other road users. However, allowing people into queues is not part of their national DNA. Re-entering the traffic will require close quarter threatening of the top layer of some car's paintwork.
Back in the vehicle lane, the first office is for Immigration. I presume that this office is also the customs desk for local vehicles. However, for carnet-vehicles, they call over the chief.