The incorporation of transition metals in GaN has long been of interest in spintronics due to theoretical predictions of room temperature ferromagnetism in these materials. However, the mechanism of the observed ferromagnetism of the nitride-based DMS is still controversial, and may originate from a carrier-mediated, defect-related or nanoscale clustering mechanism. In this work, we present a comparative study of the incorporation of various transition metals and their effect on the optical, structural, and magnetic properties of GaN. Metal-organic chemical vapor deposition (MOCVD) has been employed to produce epitaxial films of varying thickness and manganese and iron doping using bis-cyclopentyldienyl(magnanese,iron) as the transition metal sources. High-resolution X-ray diffraction reveals no secondary phases under optimized growth conditions. Magnetic hysteresis is observed at room temperature in both GaMnN and GaFeN, though the strength of the magnetic ordering is roughly an order of magnitude weaker in the Fe-alloyed samples. Increasing Mn concentrations significantly affect long-range lattice ordering, and the observation of local vibrational modes (LVMs) supports the formation of nitrogen vacancies, even under optimized MOCVD growth conditions. Such vacancies form shallow donor complexes and thus contribute to self-compensation. A disorder-induced mode at 300 cm−1 and a LVM due to vacancies at 669 cm-1 were revealed by Raman spectroscopy.