Javascript model works by repeatedly appliying forces to a mass for small periods of time and observing the results

An automatic (closed loop serveo system with proportional gain) was implemented to control the vessel and, as was expected, the system hunted.
This is due to the the delay caused by the javascript calculations.

It might be possible to eliminate the hunting by applying derivative and proportional gain in the feedback loop.

We could minimise the delay by running the model in a separate process and using the existing HTML/javascript pages to display a picture every few milliseconds.

The separate process would be written in C++. For more speed, much of the processing could be delegated the the graphics processor.
For ultimate speed, the separate process could run on a separate, dedicated PC.
 
The HTML/javascript page would read the current status of the model using HTTP - the delay involved in getting the picture will be inconsequential.

Reducing the processing time of each iteration will not necessarily eliminate the hunting completely. Derivative and proportional gain calculations my still be required.