In this paper we present a study of in-medium jet modifications performed with JEWEL and PYTHIA 6.4, focusing on the uncertainties related to variations of the perturbative scales and nuclear parton distribution functions (PDFs) and on the impact of the initial and crossover temperature variations of the medium. The simulations are compared to LHC data for the jet spectrum and the nuclear modification factor. We assess the interplay between the choice of nuclear PDFs and different medium parameters and study the impact of nuclear PDFs and the medium on the jet structure via the Lund plane.