I just fixed it! It turns out it was a power supply problem.
How it works: So basically, the converter uses the -5V line to un-invert the colors (Nintendo unisystem boards output inverted colors because of the sanyo monitors). So what was happening is my power supply is outputting -4.4V instead of -5V which is too high. So what was happening is that the sync was also at too high of a voltage causing it to have a different sync than what is needed.
My solution: I put a potentiometer on the sync line which allows me to adjust for this higher-than-necessary voltage. So far, it seems to have worked. There are still little blips here and there, but I am going on a limb and am gonna say that it just needs more fine tuning.
Thanks for the suggestion SignGuy81, all the caps on the board are fine, this is the first thing I checked. To be fair, re-capping it is probably my worst nightmare. I counted and there are more than 60 electrolytic caps and about as many ceramic ones.