When i first start the car: if the car is not reving at least 3000 rpm the brakes go all the way to the floor

While driving: brakes work fine on the interstate, but around 2-3000 rpm range *somtimes* the pedal goes to the floor.

After its been running awhile: even with the car sitting still idle at 1000 rpm the brakes *sometimes are fine*

Its like they work when they want to,could this be from a poorly done valve job and the motor is not pulling a good vacuum? I would say its the booster or master cylinder going bad but this has only been happening since i put my motor in. Its been about a month/3000 miles. And its done it since the night i started the car with the new motor in. Any help before i spend $$$ on brake system? Thanks