Vacuum pumps are OK for getting the majority of the air out of the system, but it's still a good idea to follow up with either a pressure bleeder or the old style pedal push bleeding job. I like to fill the MC and open all the bleeder screws a little, to "gravity bleed" most of the air out, then do a pedal pump bleed job. Just don't work the pedal up and down vigorously- - - -push it once and hold while a helper operates the bleeder screw.
Some disc brake calipers flex a little under firm pedal pressure, giving the impression of a spongy pedal.
Jerry
