Using our new 3-D relativistic electromagnetic particle (REMP) code parallelized with MPI, we investigated long-term particle acceleration associated with a relativistic electron-positron jet propagating in an unmagnetized ambient electron-positron plasma. The simulations were performed using a much longer simulation system than our previous simulations in order to investigate the full nonlinear stage of the Weibel instability and its particle acceleration mechanism. Cold jet electrons are thermalized and ambient electrons are accelerated in the resulting shocks. Acceleration of ambient electrons leads to a maximum ambient electron density three times larger than the original value. Behind the bow shock in the jet shock strong electromagnetic fields are generated. These fields may lead to time dependent afterglow emission. We calculated radiation from electrons propagating in a uniform parallel magnetic field to verify the technique. We also used the new technique to calculate emission from electrons based on simulations with a small system. We obtained spectra which are consistent with those generated from electrons propagating in turbulent magnetic fields with red noise. This turbulent magnetic field is similar to the magnetic field generated at an early nonlinear stage of the Weibel instability. A fully developed shock within a larger system generates a jitter/synchrotron spectrum.