Hmm. I think it's doable. It might not be relaxing but I think 3.5 isn't as bad as 2. I think your 3 year old is the challenge here.
Singapore Airlines are supposed to be the absolute best with children. When I flew to Oz I did a 3 day stopover to start dealing with the jetlag too. Singapore also excellent for stopovers with children.
My flight tips are to take plenty of food, wrap lots of little toys to open every hour, things like stickers, wikki-stix, books with magnets, crayons, toddler comics. If you can stretch to it a portable DVD player regularly saves my life on flights (all tv rules thrown out of the window for flights). Helpful on the stopover too.
I always pack more clothes/nappies/milk etc than I think I'll need, lots of spare dummies, blankies and so on.
I'm not sure about this, but I think the cribs you can get are provided for the bulkhead seats and on my last flight I couldn't move the armrests on the bulkhead seats so DD couldn't lie down. This caused a BIG problem. It might only be virgin, but it's worth checking. I suppose it's better to have the skycot but worth knowing in advance to pack a support pillow if your DS can't lie down.
DD always managed to develop exploding both ends every flight I took at under a year, so I always over pack now. Another reason for slightly overpacking your hand luggage is in case your bags go missing - I once arrived in a arse-end-of-nowhere in Thailand at 9pm and my bags remained in Bangkok. Luckily I had spare EVERYTHING in my handluggage so we survived the night until my bags arrived.
I also used to carry DD in a sling where possible, it really helped on the flights and the whole baggage/customs thing. Interesting in toilets with a backpack and sling, but do-able.
I can't help with Perth stuff, but Suzywong should be able to, she's based there.
Oh, also agree with cowmad. Lollipop for takeoff for DS and bottle for DD. I've always done this, and more often than not DD would fall asleep.
Good luck. Will you have somebody at the other end to help you deal with the jetlag? I found that the worst to be honest.
Talk to your GP about the drugs. Some children can have a bad reaction and become hyper-active, so mine advised testing a few days beforehand. Unfortunately I didn't have time, but I think I would use them next time I do a night flight - DD and I were up for about 30 hours last time and it was awful.