Thanks for the input madams, ive really had no problems with it, just the flickering of the lights which gets very annoying at times. The battery is new, the alternator is only a few hours old, so im good there. As to the wires by the battery, im not sure if I made sure those had a good connection, when I dropped in my new motor I also sanded and repainted my engine bay so I dont remember if I cleaned off those areas, I guess thats something for me to check in the morning.
Edit: I also replaced those cheesy battery terminals a long time ago with some anti-corrosive ones from auto zone, but I didnt have this problem back then, kinda odd that it would appear this far down the road, but I will check those out also.