Alex, the runup is generally done with about half the max RPMs. Somewhere in the 1700 to 2000 rpm range. When running on only half the cylinders but with full throttle, I would not be surprised to see the engine actually reach that RPM so you would not necessarily find anything wrong then.
At the start of the take-off run there should be a last check, and that's that the engine is actually achieving a given minimum "static" RPM when the throttle is fully opened. This is somewhere in the region of 2300-2400 RPM. Did you also do this check? It's a very rare engine that's able to reach its minimum static RPM with only half the cylinders operational.