Conductive polymers such as poly(3,4-ethylenedioxythiophene) (PEDOT) are used in a wide range of applications as transparent electrodes, hole injecting layers or thermoelectric materials for room-temperature applications. However, progress is needed to enhance the electrical conductivities of the materials and to provide understanding about their structure-transport relationships. This work presents the synthesis of highly conductive PEDOT-based polymers using iron(III) trifluoromethanesulfonate as oxidant for the first time. The metallic behaviour of the polymer is revealed by conductivity monitoring from 3 to 300 K. The electrical conductivity is further improved (to 2273 S cm$^{-1}$) using acids, leading to a positive temperature coefficient of resistivity at an unprecedented 45.5% oxidation state. X-ray photoemission spectroscopy (XPS) and time of flight-secondary ion mass spectrometry (ToF-SIMS) analyses demonstrate a complete replacement of the trifluoromethanesulfonate anions by hydrogen sulphate counter ions. This substitution results in an increased concentration of charge carriers (measured in organic electrochemical transistors) along with an enhancement of the mean size of crystalline domains, highlighted by small and wide angle X-ray scattering (SAXS/WAXS), which explains the 80% increase of electrical conductivity.