When you say it happens from 3000rpm and up, is that repeatable when the bike is not moving? Just rev the engine and see if it vibrates.
If it only happens when bike is moving, it is unlikely to be the engine.
Have you swapped out the wheels yet? It could be a wheel balancing issue. Try inserting dynabeads and see if it smooths out. Maybe your wheel lost a weight somewhere or is worn strangely.
Also check alignment of the back wheel, you can do the string test for that.
One guy on these forums said he had vibration that was caused by his 16t aftermarket front sprocket, but I have it on my bike now and don't notice anything, but it's something to consider.