Gents,
You're dealing with uneven pad deposits. The videos below should help you work your way through this issue, and help prevent it it in the future.
If the deposits are very mild, just driving around with the brakes cold could clean them up.
If not, cleaning up the discs with a scotch brite pad could do the trick.
Or, if you have a set of track/race pads on hand, install them and drive around cold. That will peel the pad transfer layer off in a hurry (as in the video below).
If that doesn't work, the next resort would be getting the discs resurfaced on a brake lathe.
If the deposits are really bad, they may not be repairable. That is usually not the case in our experience however. One of the above typically gets the job done and eliminates your judder.