G'day Okee. As you point out, September is not the best time to set off on a northern adventure. However, there is no real need to let that deter you. The sailors in North Queensland and the Northern Territory sail year round; as indeed do the sailors in the Caribbean during their hurricane season (which is right now).
Along the coast from Brisbane, there are many places to hide. In the southern and central part many of these places are rivers which are protected by bars and which, therefore, can be dangerous if crossed at the wrong time (tide vs wind etc). However, once you reach the protection of the Great Barrier Reef and the offshore islands such as Hinchinbrook, the hidey-holes are numerous and safe.
The major complaint of sailors in the northern parts during the Wet season is simply the heat and humidity. Even weather cocking to the wind at anchor can leave you hot and slathered in sweat in your bunk. If you choose to spend part of your time in marinas, a small half horsepower domestic air conditioner (from Big W or K Mart or similar) will cost very little and, with a little inventive ducting made from 3mm ply, you will sleep as though you were in an Arctic winter.
The practical sailing stuff: For as long as the south easterly winds blow you will have great sailing north to Thursday Island. A mere sail trim is all that's then required to take you across the top. As you move west of Gove, you will encounter shallower water, a larger tidal movement and in some cases fairly strong currents. However buying the appropriate pilot books and cruising guides will give you all you need to know here.
There is, as far as officialdom is concerned, a problem with anchoring off Aboriginal lands. You are supposed to have a permit and included in the application is a prediction of when and where you will want to anchor overnight, or to recover from a thumping after a tropical blow. On a sailing yacht that is, of course, impossible to forecast. However I have always simply dropped anchor and have never been confronted by any official.
As you close on Darwin, the currents become strong between the tides. They can run at up to six knots depending upon the state of the tide and position of the moon (and of course, how you hold your mouth). They are predictable and run with the wind when the tide is making. There are many spots to wait until near the top of the tide and making a run at those times will advance you across the charts fairly quickly. BUT...as long as you take care, there is no need to stop sailing. You may require the assistance of the iron tops'l as the tide drops.
Darwin has everything you will need to either wait until the wet season is over, or to provision your vessel for a charge north through Indonesia and on to Malaysia or Thailand.
Waiting in Darwin until mid-year is worthwhile. First because the Dry is perfection and because you can sign up with one of the rallies or races which run up through Indonesia to SE Asia. The organisers will look after your sailing permits, parties along the way and general back-up. The cost of joining one of these rallies (Darwin=Ambon Race; Sail Idonesia etc) is minimal.
For details, look at the websites for The Darwin Sailing Club and The Dinah Beach Cruising Yacht Association.
Now a word of warning. Tropical revolving storms happen across the top. In any year between Townsville and Carnarvon, there will be approximately ten TRCs. Some will develop into cyclones. That's a helluva lot of coastline for ten events and I suggest, along with most northern sailors, that it is necessary to have a good knowledge of the weather patterns, flows and strategies.....then just bugger off and go sailing!
There will be numerous squalls which will pass quickly and fill your water tanks during any wet season from Cairns to Darwin.
Finally, another reason to wait in Darwin (or Cairns..except Cairns is a bit 'agricultural' compared to Darwin), is that in the Dry, the sail north into Asia will always be either a run or a reach...never a beat.
Have fun and please keep us appraised of your progress.
PS at the risk of repeating myself, I offer you this link. Its a great real-time planning tool earth :: a global map of wind, weather, and ocean conditions
PPS. Don't wait too long is you want to head north soon. In November, you will encounter some northerlies and while that makes a southerly run a dream trip, it makes a northern run a pain in the bum.
PPPS. It would be a real shame to go north to Darwin without then taking a side trip (more westerly) to The Kimberlies and in particular to the spectacular King George River. Sailing back can be a challenge over a two day period, but it is well worthwhile.
PPPPS. As for sailing east after Malaysia: Across to Kota Kinabalu and the Philippines is a bit tricky, but is not hugely challenging. Going north then to Taiwan and Japan is a pleasant though moderately challenging sail (especially if you fail to outrun a hurricane north of the Phils as indeed someone, who looks and sounds very much like me did, some time ago).
The trip across the Pacific can then be a true challenge and the strength of that challenge is why most people opt to sail to the USA by 'going around the back'..ie via the Mediterranean. Buy a copy of Ocean Passages for the World (New or used from eBay; but not the 1973 version as it was missing the fold out maps and charts) and look at the traditional sailing route across the North Pacific (just below the limit of ice) and you will discover there is a nifty current to assist your passage through the icy hell you are perhaps contemplating. It's a quick way to the west coast of the Americas in much the same way as the shortest route between Cairns and Perth is straight across the middle. There is of course the southerly route via the roaring 40s. Check southern ocean sailing Volvo Around the World racing for an example of just how pacific, the Pacific can really be.