To perform a proper benchmark, you should tune the CPU and GPU frequency to the maximum (i.e, minimum and maximum is 1.2GHz for example). Anything lesser than that will lead to inconclusive scores.

You can use ChainFire's Benchmark or Antutu as a yardstick, but don't dwell too much on the scores. Some tweaks like the I/O scheduler might be worse off as it seeks to balance the synchronous and asynchronous processes that might affect what the outcome of the benchmark is

Edit: The one thing you can measure though, is the battery life and smoothness of your day to day operations, as those are the ones that actually mean something to you right?

It doesn't matter if your benchmark scores are the highest, but scrolling to a screen is laggy. (I could make ThunderBolt! be a good performer on benchmark, but your battery and performance would be bad).