Here is the above instructions in image form that should work on the '96-'00 4Runners:
And yes, getting the bench bleed on the master correct is necessary. It has a balance system in it that is required to get the front discs and rear drums to play nicely together.
You may also have some air in the ABS system that needs to be removed.
I'm in the middle of a brake bleeding saga myself. My brakes are back to about 80% of where they should be after a new master cylinder and Tundra front brakes. Need to re-bleed to get some air out of the ABS system at the moment.
-Charlie
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'99 4Runner SR5 Auto -
4WD swapped
'89 Camry Alltrac LE 3S-GTE 5spd
'17 Chevy Volt Premier
'16 Honda Odyssey Elite
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