Some reason why most operators do not use flap 40 all the time (landing distance not an issue) is because it increases wear on the flaps, makes more noise and in gusty conditions you may get the flaps blowing back to 30 through the automatic flap protection system.
Autobrake max is quite agressive so only used if really necesary, not that comfy for the pax.
I would think a 6000' runway would be flap 40 and autobrake 3 plus some reverser if either wet or a short turnaround to follow.
Remember that if at the planning stage you should be able to stop in aprox 60% of the available runway, this means that in reality you should be able to use autobrake 3 and use the whole runway.