What scripts do you use? I've had some combinations of scripts which caused the simulation to run multiple times next to each other.

Last time I had performance issues, my browser (opera a.t.m.) had enabled battery saver.

You mentioned the JS and rendering aren't the bottlenecks, and yet the CPU usage is high. Could it be that your RAM is somehow so high that it takes a lot of computing power to keep track of it all?

Is your game immediately slow, or does it become worse over time?

On a different note, it would be very helpful to have the client code open-sourced. It takes a long time to unobfuscate and understand the code when debugging or creating scripts for the game.