You have an air leak in the induction system. Basically there is more air getting in than the ECU thinks, the mixture starts going lean while on closed loop so the ECU chucks in more fuel, it balances out and starts to over-rev, goes too rich and then the revs drop as it starts to choke up. Then it starts to go lean again, eventually it all sort of balances up and the revs settle. Blipping the throttle and taking the ECU out of closed loop mode resets the whole process.
My son's Sei is doing the same but I'll be damned if I can find the blasted leak!
In reality it can only be one of a few places - the inlet manifold to head gasket, the manifold to throttle body gaskets (both of them) or the throttle body itself. On an 899 this is simplified a little but the fundamental problem remains. Check all of the joints that you have separated in the process of swapping the throttle body and spacer plates around.
Make sure the throttle isn't too tight as well, the engine tugs on it very slightly when it revs and it doesn't have a little slack it can go a bit mad.