Richard,
I found some clues about the little board on the Timebase board. It is named "ERD Shift Adjust." ERD is a digitizing mode called "extended real-time digitizing." The little board allows for additional vertical offset correction to the CCD output depending upon the time/div. Without it, you will see a small but irritatingly noticeable vertical shift to the waveform as the time/div is changed in the ERD range. Apparently the original adjustments were not quite enough to cover the entire ERD range. I recall, from long ago, that some of the CCDs produced more voltage offset than others depending upon the clocking frequency; something to do with variations in transfer efficiency. Usually CCDs were clocked at a fixed rate and the offset is adjusted or cancelled by some external circuitry. ERD mode will operate the CCD at a rate unique determined by each time/div setting; hence, the extra offset adjustment. Anyway, that board is standard equipment on later units and not a custom trick for a special customer.
I don't know what the other mod is that has four wires soldered to the CCD. If you are able to tell me which CCD pins, I might be able to find a clue.
Clark