@SeniGreg,
Kalimantan has been in my bucket list and even though I am on the same island of Borneo, I can't ride over to Kalimantan as Indonesia requires a carnet de passage for foreign vehicles.
I heard that there is a way to overcome the Carnet requirement by getting the Indonesian motorcycle club to officially invite you and by that you do not need the Carnet at the border. The only problem is that they do not invite solo travelers per se. Got to be big group of bikers.
So, the only way for me to ride in Kalimantan would be to rent a bike in Pontianak, Kalimantan which is the nearest city from Kuching.
I haven't done much research on this yet but I might do it next year after my Sumatra trip if I can find a bike to rent.
As to the question of which starting point from East Malaysia to Balikpapan - if you ship the bike from Port Klang to KK (Kota Kinabalu) you could do a loop of Sabah before going to Sarawak via Brunei's new bridge.
I might be partial as I am a Sabahan but the road from Tawau to Keningau has wild pygmy elephants crossing the road if one is lucky. I've done this road a few times and only seen elephant shit on the road! LOL
The other attraction would be going to Kinabatangan on the East Coast of Sabah where you can spend a few days at the Kinabatangan river and take a river cruise to see wildlife such as Proboscis monkey, wild orangutan and pygmy elephants. The last time I did this was a long time ago like maybe 20 years back?
I've included a snapshot of the route if you start from KK.
If you start from Kuching you are close to the Kalimantan border and can proceed to Balikpapan.
If you are an Aussie and a history buff, Sabah has a special significance for Australians because of the Sandakan Death March. Google it if you are interested.
Brendon