When you say you bleed the ABS pump, you mean you open the exit bolts, then open the calipers, and pump until the bubbles have traveled from the ABS all the way out. Is that right?
No, everything is tight and closed, all bleeders, and all line bolts.
(This is After you have refilled the lines by vacumming fluid through, and fluid is coming out of all bleeders when they are opened).
Bleed the front calipers, then the front mc, then the abs exit line bolt(open/close the line bolt as if it were a bleeder screw. Wrap a rag around it while you do it, to keep the small amount of fluid from getting on the bike).
Bleed the calipers, they should bleed as normal.
Bleed the MC, it should appear to bleed as normal, only when you release the brake lever, you will see the fluid level in the MC resivor cup rise right before your eyes...and that is the air in the line from the mc to the abs pump that is causing that.
So pump your front brakes, and then bleed the abs exit line bolt.
After you bleed the calipers, the mc, and the abs pump, then go back to the mc, and finally the calipers again.
I prefer to tie the lever to the bar for several hours and bleed again.
When doing so, I bleed the calipers once each, and the mc's once each, and it's done.
Do the rear brakes the same way.
It also does not matter if you do the front or rear brakes first.
Just keep in mind that abs brakes bleed the same as non abs brakes, only that you need to bleed the abs exit line bolts after you bleed the mc's.
And, if a mc does not have a bleeder, simply use it's brake line bolt as the bleeder instead.