I have recently replaced my relay switch thinking that may have been the problem since the wiring somehow got burned inside. After doing so it seems I am not getting any current to my thermostat. I only have 2 wires to my thermostat to begin with and I am wondering if its wiring in the furnace or if its just a circuit breaker. What are your thoughts

If you cannot sound out the problem with a meter you better call for ON SITE service. You never know what else got burnt. It could have been hit by a voltage surge causing other problems.