If it only happens while riding when trying to accelerate from very low revs - 2000 is very
low revs for this engine - I would say you are lugging the engine and that you absolutely need to change your habits to stop doing this. However, you say this:
...when I put it on the race stand, put it on 1st gear and let the wheel run, it judder like crazy, but soon you open the throttle the judder gone...
Which leads me to believe you are not lugging the engine. This is good, because besides running it without oil, lugging an engine is one of the worst things you can do.
Lugging an engine is like hammering the engine parts with every explosion in a cylinder. It racks on the rod bearing/journals, makes the pistons slap the side of the cylinders hard, and if is done enough, could probably break piston rings. It also creates a hammer effect all the way through the drivetrain. There are springs in the friction disk (of the clutch) which takes up some of this hammering, but they will only take so much before they wear out as well. This causes premature wear all the way around. It's not like it will wear out tomorrow, but it will cause wear over time. If you want your car to last a while, you don't want to be doing this.
If your "judder" only happens at very low speeds in gear with the rear wheel spinning - like when you had it on the stand - then MacBandit is probably correct (good odds of that since he is an actual bike mechanic), and the judder is due to your chain, and or sprockets. If it happens at similar revs in neutral, without the chain and wheel spinning, then it's probably engine related.