Where do I start. If you go to the Bungles, its a long way to get back to the GRR as the Bungles is closer to Halls Creek. Your option there is drive down to the Bungles and head straight along the bitumen to Halls Ck, Fitzroy xing and Broome and Exmouth. Head back to Broome , up to Derby and spend the rest of your time driving the GRR. You won't see much as time will be short. I suggest the following based on having driven and lived it for 5 weeks.
Windjana
Tunnel Creek
Bell Gorge
Mt Barnett
Mt Elizabeth
Home Valley.
Haven't been to ElQuestro$$$.
If you had time Mitchell Falls is brilliant.
My suggestion is forget Exmouth and head straight to Kununurra and hope onto the GRR. Even to do it quickly will chew your days up. When you get to Broome head back onto the Great Northern and stop in at the Bungles on the way home.
My 2 cents. Have a great trip.
Wayne
Thanks Wayne. That's very helpful. Just to clarify though, Darwin is not home and we won't be coming back this way ( at least not immediately). After swimming with the whale sharks in Exmouth (which is not negotiable,unless you want to explain it to my better half and think you can survive!) we have only a few days to get to Perth for a job interview. The 2.5 weeks is our time limit for getting from Darwin to Exmouth, one way.
It sounds like we may have to give the Bungles a miss this time, so I guess we need advice on the best places to see and stay on the GRR. Our first day will be a short one with an overnight at Edith Falls near Katherine.
To explain what we're doing and why our schedule is so tight - my partner is a nurse and she can easily get three month contracts in rural / remote australia, and those contracts include accommodation and a travel allowance. We are therefore limited to travelling to wherever she finds work, and fitting in as much as we can in between those contracts. We can't see everything, not at one time, but we're seeing more of Australia this way than most people our age (I'm 40, she's 39), and get to explore the towns where we work for three months quite well. Because of this unique situation, we focus on what we can fit in, rather than what we can't (we will get back to those places another time). We are happy to put in a few long days of driving in order to see something special, but don't want to over do it.
So far we have driven from Melbourne to Alice Springs, via the Oodnadatta track and Dalhousie Springs, and spent four months in Alice exploring all the sights on our weekends. From there we took two months off and travelled east to Yeppoon, then down to Brisbane for a week and further south to Bermagui for a few weeks over New Years. Then back through Kosciosko NP, Alice Springs and up to Darwin for three months. Now we plan to explore WA as much as possible, although we don't know where we will be based for our next working leg....
Not conventional, i know! Maybe in 20 years we'll do it again in the more conventional grey nomad way.

Thanks to everyone for your advice.
Cheers,
John