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I understand that your bike has stood for a while? If the pads have sat in the same place on the discs for a good while it could well have caused the surface of the discs to have oxidised differently under the pads to the rest of the surface. This will cause the juddering that you report (unless it's actually warped discs).
I would thoroughly clean the discs and pads with clutch and brake cleaner to get rid of any contaminants, including the invisible ones. Then take the bike out and on a good clear straight road, get up to a good speed and apply the brakes firmly and hold on for as long as possible. (Watch your mirrors!) Don't come screeching to a halt, but rather let the brakes off gently without coming to a stop and then repeat the process again if possible. The idea is to get the discs and pads nice and hot and apply plenty of even fiction.
It's always worked for me. Sometimes you can get this pulsing thing after just washing the bike. The pads will hold moisture to the disc and make "rusty" spots with a different friction co-efficient which is what you feel.. Slip, grip, slip, grip ect.
If the discs are warped then measuring with a dial gauge is the only way to check, and if that's the case your disc Doctor might be the way to go if he's cheaper than new discs.
Some might tell you to clean out the bobbins, and they could well be right, but that has never worked for me, although I can't see it doing any harm, especially after a lay up.
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