If you say that you've made some modifications with composite video amplifier - may be it would be better to check them again)
I don't think that you have problems with the chip if in the PAL mode the picture is OK.
As far as I can see you have 2 quartz resonators on your plate. Is it a "default" set or you've installed the second one?
Maybe you'll need to check k1, k2, k3 switch pads closely.
And what about S-video... I know that some people disassemble the composite video output in order to make an S-video one. Is it an option for you?)
Upd: In my MD2 clone everything is simple - take a breadboard and do whatever you want (see the creepy image below
))
On the picture below you can see the scale of my mod: left pin is luma (Y) the middle one is GND and the right one is chroma (C).
I've never seen a genesis 3 clone but, IMHO, the roadmap of the process would be the following:
1) make a mod on separate plate/breadboard piece;
2) cut chroma and luma tracks from pins 52 and 53 to insert 2 switches similar to O/J or N/P in order to switch between s-video mod and composite video and place them in available place e.g. in the bottom holes;
3) connect the output s-video signal to md2 av female connector (and make the custom cable) or provide a separate case-attached s-video female connector (the second picture).