It could possibly be warped discs. I'm afraid I would put my foot down and make the dealer check the bike earlier they sold it to you and they are responsible for it. it doesn't take a tech five Min's to check for a warped disc if they are they can order new discs and pads in time for when you have it booked. Does the lever pulse when you get the judder (you'll feel the brake lever pulsing in and out slightly), If so you are looking at warped discs no question, if not the brakes may need cleaning or the front forks may require attention or adjustment. I'm betteing on warped discs. Don't take crap off your dealer they sold the bike they fix it and make sure it's quickly new discs could cost upwards of £300. I've had a couple of GSXR discs warp but only on trackdays and always always found EBC prolite discs and matched HH pads work well and be cheaper than STD.
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