Arriving at 9.25 am is a lot better than 6 am and 18 Nov. is just after the Melbourne Spring Racing Carnival, the Melbourne Cup you have missed by 11 days but it is a time renowned for gardeners at the track having roses blooming right on time and gardens around Melbourne ought to be looking their best.
As for the checked luggage, I'd just double check with your airline that it is checked through for you and my allowance of time for exit etc. was just in case it is not checked through but with your backpacks and even if having no luggage, you are still subject to customs and will have filled in an arrivals card as you are accustomed to.
You can either have things to declare or not but either way you can still be selected so as far as what you may have, even stuff like snacks needs to be declared as food, even a piece of fruit from the plane needs to be discarded in bins provided on disembarking.
If you have things you should have declared and forgot and get picked for inspection, you could be up for some time to clear customs.
As for the City Circle Tram, it as far as I know from past use no longer goes down Spencer Street outside the Southern Cross Station so unless that has somehow been changed back ( which the route does not indicate ), you can walk a couple of blocks south, flat and then downhill to Flinders Street and you will see a stop there to the left at the intersection.
I would not get too ambitious with tavelling too far out of the CBD as like over to St. Kilda for time flies quickly when you least do not want it to and then you can be in a rush to get back to the airport, a taxi then the best option so perhaps if you use Skybus to go in, you might just consider getting a one way ticket.