Nick -
The alignment pattern working would seem to indicate the CPU can read & write RAM just fine, nor are their issues from the CPU to the DACs. I'm pretty sure the digitizer writes directly to RAM, and since the pattern isn't dependent on the signal or sweep, I'm wondering those gaps are an addressing problem between the digitizer & the RAM?
But yeah, check those supplies first, and if it's still lurking, we can keep digging.
Cheers,
Paul