Pull the reservoir out and dump it.

After I do a flush it usually won't fill all the way back up. Just fill the reservoir, put the cap on and start driving. After a few driving cycles the radiator will suck in fluid as needed (whenever the cooling system cools). Just check the reservoir periodically and add more as needed.

Also, the factory thermostat has a jiggle valve in it presumably to help bleed air through it, which might help a bit.

'97 4Runner, '06 F350, '86 4Runner, '05 WR450
http://home.4x4wire.com/erik