Since you fixed the broken wires have you made sure that you do not have the “passenger window lock” still turned off.
This would still render those window controls off.
But if you are using the drivers control panel…it would make this a item to ignore.
Another thing; You say that you tested continuity!!
Yet, you mention that you are unsure where these wires lead.
But continuity is testing one wire from point A to point B .
This still is not a perfect test if a wire is broken inside of the insulation.
These can come and go as you move a wire or close a door etc…
Yosemite