We're in Indonesia now, started from Europe, travelling 2-up on a Vstrom650.
1. Is the bike ok, an st1300 (done Europe on it easy) but overland to Aus?
thinking more about the type of roads we may encounter rather than bike itself.
Sure the bike is ok, very reliable I'd think, but maybe a bit heavy sometimes. Freighting such a big bike will also cost more, especially if you go by air (and you will most likely need to freight it between India/Nepal and Thailand, because you cant go to Burma (or you can try doing China, but that'll be expensive).
2. what is the best time of year to start from the UK?
We started in 9th October (From Finland to Germany, then down to Greece, then Turkey). Weather got a bit cold in eastern Turkey, but otherwise it was actually quite nice, and steadily warmed up until it was steaming hot in southeastern Iran (that was around mid-November).
It does get very cold in Turkey and Iran in midwinter, so better go through before that.
Then think about the rainy seasons in the tropics; and also that they will be the other way round in southern hemisphere. We've actually hit the Indonesian rainy season quite hard, with lots of rain and floods in some areas. Would probably be much nicer (drier) to ride here in June/July.
3. Is there a best route for riding two up?
Turkey-Iran-Pakistan-India is quite ok 2-up (surprisingly maybe the worst roads we found were actually in India); and there are some places in India where you'll probably wish you had a lighter bike with more ground clearance!
Thailand and Malaysia have excellent roads. Indonesia is a bit of a challenge, but if you stick to the main roads, shouldnt be a big problem (may get a few new scratches to the bottom of the bike, but after India they wont matter!) Havent been to Australia yet, so cant comment on that.
4. How much time should I allow for the trip
We allowed 6 months, but are now feeling we should have at least 2 more months. Depend on how fast you want to go on. Anyway there is so much to see and do, probably cant do it all on one trip.