When it happens, does pumping the brakes help? Does the pedal come back up quick or slow? Hydroboost is just that, hydraulic boost for the braking effort, it's possible the new pump is making a good bit more pressure than the old one and has killed the master cylinder. If the hydroboost dies, you still have brakes, the rod goes straight through the unit, they are just VERY stiff.
If the pedal comes back up normally, and pumping helps, you have a bad master cylinder. If the hydroboost were dead you would be using both feet on the whoa pedal. Since you say they work intermittently I would start with the master cylinder. Get two BIG jugs of brake fluid and a buddy, once you have it bench bled let it gravity bleed for about an hour, then start pumping. You really want to flush the entire system well to get all the particulates and old fluid out.
