Route Suggestions – Cooktown to Sydney via Outback / Inland

You seem to have picked the routes I would consider when returning from the far north. By the time you are returning, I don't think flooding would be much of a problem. To check on any likely problems, I would consult the site QLD Traffic. This will allow you to pick a route home with the best roads.

Some of the first few towns are underwater from the ongoing floods and its only going to get a lot worse unfortunately

I've done Route 2 a few times from my home in Tamworth. However, unless you have a desire to go through Tamworth, instead from Goondi I'd go down to Narrabri onto Boggabri, down the "Grain Way" to Mullaley, then down Black Stump Way to Coolah and Mudgee.
Reason is that its slightly shorter , quicker and primarily flatter, hence easier driving.
You can stay at Boggabri.
Far too early to have a definitive route until you ascertain flood damage on the stretch from Winton to Cunnamulla in a month's time. Good to see you have alternatives.
I don't believe anywhere on Route 2 south of Charters Towers has had excessive rain ( just from looking at rainfall not consulting Road Condition sites).

At this point, Route 2 would be safest and scenic enough. I personally wouldn't go down the coast route---too many people. Even if flood waters have subsided further west, road conditions and maintenance could well be an ongoing concern. As stated above, keep checking closer to time of leaving via relevant govt. websites. Also, check local shires, van parks, etc. for eye-witness reports.

Thanks for the feedback. With Route #3, would it make sense to detour from Roma > Lightning Ridge ? Also, from the listed towns in this route, where would you recommend staying multiple days? Cheers

At present some or if not all of the inland routes through middle QLD you have selected are experiencing flooding or are on Flood watch..you will have to check with the road authorities for up to date information if you still want to use those routes.
I know the coast route, it is a brain deadening experience, boring a bat shite, crowded with traffic but given the circumstances the least likely to cause major delay.
You could come down on the Bruce as far as Gladstone then head inland along the Burnett Highway A3 down to Toowoomba, get on the New England Hwy down to Sydney.
I have travelled that route a few times, Gladstone down to Toowoomba and have found the road condition quite good, lighter traffic and is quite scenic.
The New England has improved as most of all the major interstate truck movements are along the M1 freeway, it can be still busy, but there are heaps of places to stop and have a break.
Good luck.