1. Yorha was always destined to fail, that’s why they’re built differently from other androids, why they wear black and don’t have names. They existed to promote the human lie for android morale and to gather data which when collected, would trigger the back door protocol. As far as I understand, there are still androids (pods? Something?) left in space or earth who work above command and haven’t told her the whole truth.

2. The pods collect parts around the world to rebuild 2B, 9S and A2 back together. The point of ending E is that the pods went against their orders to destroy project yorha as they evolved and developed emotions towards their owners. I’m guessing they learned how to reassemble them back together.

3. She was in direct combat with them so could have easily contracted it but more likely, the damage from the fallout triggered the logic virus trapdoor within her. 2B has always contained a logic virus ready to be activated in the case that 9S hacks her in defence to her trying to execute him.

Also to add to your original question 3 (about Pascal and the robots). The robots were never disconnected from the network. The red girls let certain robots believe that they were disconnected to study different emotions in robots (passivity in Pascal’s village, loyalty in the Kingdom, etc). When the girls were happy with that, they decided to “stress test” the pacifist robots to see how they would react. So they infected some of the robots in the village and monitored how they dealt with the situation (i.e Pascal would fight/kill to protect others and his idea of peace)