I had exactly this on my 999, same kind of speed also, from around 55 down to say 45 the front end shook it's head all over the place, was a real pain as I travel through a lot of 50 limits.
To be honest I just ignored it, but I did change a hell of a lot on the bike to get it set-up for me in the meantime, ride height, head angle, springs front and rear, but the problem still persisted until I recently replaced the tyres (F+R) and voila shake gone, I'd done less than 2000 miles on them also, just fried them on track.
Might be worth a shout, even if it doesn't fix the problem you'll still use the tyres.
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