Can't get air out of brake system
 

My friend has a 2016 FRS. He accidentally got air in the system by letting the fluid in the reservoir run low during a flush.

He bled the car the old fashioned way a few times. We also tried using a vacuum evacuator which is the method I've used multiple times on my BRZ PP and Miata, and I always get a firm pedal that way. Didn't work for his car.

The car still has an initial soft pedal, for maybe 2 inches off the top. The brakes still work ok. The second pump is really firm and how it should be all the time.

Do we need to cycle the abs pump to fix this? Any other suggestions?

No. Don't mess with the ABS unit. Unless it is triggered while air is actually in key places, its internals will not be exposed.

Go with a bench bleed of the master cylinder.

before you take off the master, try pumping it up and cracking open the lines on master cylinder one at a time, I normally don't have to bench bleed it. When I have customers come in w/ broken lines and dry reservoir, I normally bleed the master in the car, do the calipers and then I'll active the ABS a few times if the pedal doesn't feel right. but thats my 2 cents

How to you activate the abs? By driving and flooring the brakes or with a scan tool?

you'll need software, try the bleeding the master and doing all the calipers again. if it's still not there I'd just bite the bullet and pay a respectable shop their hour labor or w/e and have them plug into and do it.