If a section of the master runs dry, you need to gravity bleed the section(s) at each wheel until there are no bubbles at any bleeder, (might take a quart or more of fluid). Then do the automated bleed, gravity bleed again, then bleed as normal at each wheel.

The automated bleed operates all of the solenoids in the ABS unit. It pushes any air that was trapped, into the lines. If you pump the pedal, any air that the automated bleed pushed out will get sucked right back in. That's why you need to gravity bleed, then bleed as normal after the automated bleed. Unless you have a power bleeder, ($$$) this is the ONLY way to remove all air from the system.

 

Not saying you are wrong, but I have never had an issue pumping the brakes on my 2000. And The pedal is nice and firm. I have never run the MC dry either, I always keep it full when bleeding. Also, I have tried to gravity bleed the lines and it takes forever.

 

The problem is when the master cylinder runs dry, air enters the ABS unit. As long as it doesn't run dry, pumping the pedal is fine, as long as you do it slowly.