Model-independent constraints on modified gravity models hitherto exist mainly on linear scales. A recently developed formalism presented a consistent parameterisation that is valid on all scales. Using this approach, we perform model-independent modified gravity $N$-body simulations on all cosmological scales with a time-dependent $mu$. We present convergence tests of our simulations, and we examine how well existing fitting functions reproduce the non-linear matter power spectrum of the simulations. We find that although there is a significant variation in the accuracy of all of the fitting functions over the parameter space of our simulations, the ReACT framework delivers the most consistent performance for the matter power spectrum. We comment on how this might be improved to the level required for future surveys such as Euclid and the Vera Rubin Telescope (LSST). We also show how to compute weak-lensing observables consistently from the simulated matter power spectra in our approach, and show that ReACT also performs best when fitting the weak-lensing observables. This paves the way for a full model-independent test of modified gravity using all of the data from such upcoming surveys.