Here are some general notes to consider.
The NE Monsoon tends to blow at its hardest around that time (similar to the Xmas Trades in the Caribbean) so favoring the west coast
of islands will give you the most protected sailing conditions.
With 3 weeks and about 600nm + 25% seaway direct, there is plenty of time to reach KK
on W. Coast of Palawan is well marked and the South China
Sea is heavily patrolled so it is the recommended route
My Map shows a suggested trip plan, which you can vary depending on conditions
90nm from Subic to Puerto Galera and Hamilo Cove breaks that up into 6hrs for first and 2nd day to get your non-sailors adjusted.
PGYC is a very social yacht club and with many dive resorts in PG, easy to go diving
2 days run down to Pandan resort where you can organize a dive to Apo reef or head
across directly to Busuanga/ Caluit Island.
There is a great Game
Farm to walk around at Caluit and very protected anchorage, where you can get a nice feed of crabs.
Sangit Resort and others can take you diving on Japanese Wrecks, but if time is an issue, worked down the lee side of the islands towards Halsey Harbor, where you can also find wild Tiger Prawns to enjoy and spectacular diving……thus making your way with least seaway towards El Nido.
Port Barton is a nice and well protected stop with Turtle Sanctuary, healthy Corals, teeming with fish
, deserted Beaches with very friendly dogs
My last rest stop would be Ulong Bay on the way to Malaysia
as it is a Naval Base and well protected.
Personally, I would clear in to Sabah at Kudat rather than KK, as I love the place, but you may have time constraints by then.
Hope this helps.