I have my doubts it's an alignment issue, sounds more like a rotor issue.
Many drivers confuse rotor warping, or warped rotors, with a condition called DTV (disc thickness variation). DTV occurs when a vehicle brakes are serviced and the brake rotor has runout in excess of 0.1mm or 0.004". This runout causes the pads to contact the rotor when the vehicle is being driven "off brake" and after 3-4000 miles, a thin spot develops on the rotor. The rotor runout itself does not actually cause a vibration. It is the effect of the thickness variation of the brake disc or brake rotor under braking that causes pulsation. Even small thickness variations such as 0.01mm will exhibit itself as pulsation. A warped rotor is a very rare occurrence and in 30 years in business, we have seen no genuine cases of warped brake rotors.
The general guideline is that if the vibration happens immediately after install, there is a quite severe runout problem that needs looking into. Brake discs or rotors should be mounted on flat smooth rust and dirt free hub flanges without the use of coppaslip which includes small particles which have the same effect as dirt. Remember that even a small particle of 0.001" under the rotor surface can cause a deviation of 0.005-0.010" at the
pad contact point.
If the vibration happens after 3-4000 miles, this is a clear indication that DTV has occurred which is not a warranty condition. The only solution for this is to remove the brake rotor, have it turned by a machine shop, or replace it with a new rotor
Are you feeling this vibration when you are on the brakes or all the time? When you put your wheels back on, did you make sure you tigthened the bolts in a star pattern to the same torque value?