The jumpers are on every 6128+ as far as I know. They seem to be solving a ground loop issue. I've never tried, but my guess is that the disk drive becomes unstable if you remove them. I don't think they solve any RAM issue, they just happened to use the ground pin of the RAM IC because it was easy to access from above.
I've never looked into the other bodged resistors / diodes, so I've no idea what they are solving.
Bryce.