You don't get things flat with a brush although it's obviously a good start. What I use on anything I want perfectly flat is an oilstone although it does rather help being an engineer that I've got a workshop full of things like that. You've only got to leave one tiny high spot of rust somewhere and the job's stuffed. It's also easier if there are no studs sticking out of the hub.
If it were the disks wouldn't you think the judder would start immediately after they were changed rather than soon after?
It's a decent figure but you might be able to do a bit better. I suggest you whip the wheels and calipers off. Clean the hubs and disks again with 80 grit and an oilstone if you have one, mount each disk on its own with spacers if needed if the nuts won't hold them without a wheel on and check the runout on both sides of the disk with the disks in different positions on the studs until you get the lowest readings. Sometimes just moving the disk round relative to the hub studs will even things out. Then mark your chosen mounting positions with a pencil. A small sharp chisel helps find any high spots if you have no oilstone. A very light smear of copper grease will ensure things don't corrode together.
If you have a micrometer check the disk thickness at different places although an error here with a new disk is very unlikely.
If you didn't also change the pads then the situation might not be ideal. Pads and disks invariably wear at a slight angle (higher surface speed out at the periphery) and with only one new component the pads won't be making full contact.
Make sure the pads are properly seated in the calipers.
Then check wheel bearing play carefully. This can exacerbate other problems as can play in suspension bushes. I had an old Marina 30 years ago which went through a godawful bout of wheel wobble at 60 mph which no amount of balancing would cure. My mate at a tyre place even tried balancing them on the car but no joy. It was play in the wheel bearings which a quick clean, regrease and tighten up properly fixed completely.
Once you've got it all together find a quiet stretch of road and in second gear give it full throttle and use the brakes with your left foot to hold the speed steady for 10 or 15 seconds if you can to bed things in. Make sure you then don't have to brake again at a junction and hold them on until they've cooled a bit. Then try a high speed stop and see if things are improved. However with runout as low as you already have it's unlikely to be the disks or at least just the disks. Problems can often be a combination of smaller faults in more than one place.