This sounds good. If I understand correctly, you only have the PAL PIF connected at the moment?
The HDMI mod will definitely fix your problem. I think you have a 50Hz video signal with the colors at NTSC carrier frequency at the moment. If you swap some of the crystals as well it should fix it I guess.
Most modern TVs can handle 60Hz with colors at NTSC and PAL frequency. 50Hz with color at NTSC frequency is probably very uncommon/does not exist.