We ended up in Puteri Harbour (middle left of map). We easily cleared into Malaysia and then had a nice visit with some old friends from Edmonds, Owen and Carrie, who arrived here with their kids on their sailboat Madrona about 5 years ago and now live here and teach at the local American School.
Clearing in is very simple, almost all handled by the marina office. We received a 90-day visa.
The marina is clean and has nice docks with easy, wide fairways. For those that don't want to go into the marina, you can anchor out in front of it and pay a nominal daily anchor/dinghy fee and get cleared in through he marina office. As I understand it, the customs and immigration officials, located nearby at the ferry dock, will not clear in walk in cruisers.