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Understanding how the release of stored magnetic energy contributes to the generation of non-thermal high energy particles during solar flares is an important open problem in solar physics. Magnetic reconnection plays a fundamental role in the energy release and conversion processes taking place during flares. A common approach for investigating particle acceleration is to use test particles in fields derived from magnetohydrodynamic (MHD) simulations of reconnection. These MHD simulations use anomalous resistivities that are much larger than the Spitzer resistivity based on Coulomb collisions. The processes leading to enhanced resistivity should also affect the test particles. We explore the link between resistivity and particle orbits building on a previous study using a 2D MHD simulation of magnetic reconnection. This paper extends the previous investigation to a 3D magnetic reconnection configuration and to study the effect on test particle orbits. We carried out orbit calculations using a 3D MHD simulation of separator reconnection. We use the relativistic guiding centre approximation including stochastic pitch angle scattering. The effects of varying the resistivity and the models for pitch angle scattering on particle orbit trajectories, final positions, energy spectra, final pitch angle distribution, and orbit duration are all studied in detail. Pitch angle scattering widens collimated beams of orbit trajectories, allowing orbits to access previously unaccessible field lines; this causes final positions to spread to topological structures that were previously inaccessible. Scattered orbit energy spectra are found to be predominantly affected by the level of anomalous resistivity, with the pitch angle scattering model only playing a role in isolated cases. Scattering is found to play a crucial role in determining the pitch angle and orbit duration distributions.