You've got two separate challenges there - VGA scan rates and greyscale. Try to separate the two in your thinking as much as possible.

For example, are you feeding the analog board variable voltages whilst still using it as a scan generator? So I assume you're looking at a blank (grey) screen, and that when you tweak the voltage up and down, you can see the screen getting brighter and dimmer. That would seem to prove that greyscale is possible.

If you have a Windows or Linux machine handy, there's software about that will give you pretty fine control over the video card. I don't recall offhand any names. But anyway, if you can rig up an adapter cable from the (cheap, expendable) video card to the analog board, and set the screen size and refresh rate to match the existing setup in the Mac, you can prove further that greyscale works, by looking at an actual image.

As far as adjusting the scan rate for VGA, I can help not at all there.

BTW bolle mentioned the poor man's greyscale project- link