The structural organization and its effect on conducting pathways in lead phthalocyanine (PbPc) thin films, a nonplanar phthalocyanine, deposited on Si and highly oriented pyrolytic graphite (HOPG) substrates in the presence of iodine and ammonia vapors are presented. Two-dimensional grazing incidence X-ray diffraction studies reveal that the crystalline ordering in pristine PbPc films on Si and HOPG substrates undergoes a drastic molecular rearrangement and surface reconstruction upon iodine doping. The structural rearrangement leads to morphological changes and higher surface roughness in iodine doped PbPc (I-PbPc) films. The obvious enhancement in the current values of I-PbPc is attributed to the introduction of holes as charge carriers. Nanoscale current mapping reveals the presence of percolation pathways in I-PbPc films, on both Si and HOPG substrates, being responsible for the observed high conductance in contrast to the isolated conducting domains in the pristine PbPc system. The broad distribution of current values across various conducting domains on Si is attributed to a mixture of crystalline phases and disordered fractions of I-PbPc, while the narrow distribution of current values observed in the case of HOPG arises from the majorly disordered PbPc molecules. These films also show enhanced sensitivity towards ammonia that is almost four times higher in magnitude than for pristine PbPc films. The current maps show that the adsorption of ammonia molecules disrupts the iodine percolation pathways, thereby imposing a detrimental effect on the conductivity of the PbPc films.