Did you plug the Shaft holes on the intake manifold too? Maybe epoxy? I left mine open and my car runs like shit.
I too did this mod last weekend.
My intake valves were not that dirty at all. The butterfly valves were dirty. I broken every one of them removing them.
I put an oil catch can on.
Throttle body coolant bypass.
Changed both Oxygen sensors.
Runs great. Much better without the VTCS and I'm happy I did it. Now, to see what the gas mileage improves too.