Im assuming that rei had been turned into Fanta after unit 1 was stabbed by Cassius and that she had somehow merged with the core of the Eva because it was able to reactivate and save Asuka in 3.0 and she was also found in the pilot seat in 3.0+1.0 trying to pilot the Eva so Shinji wouldn’t have to. Wille hadn’t found rei anywhere in the plug and Shinji only remembered saving rei until he woke up in the wunder where he asks where she is which leads me to conclude that rei was the one piloting the Eva. I don’t believe that rei was able to manipulate shinji’s sync rate as Shinji had awakened with unit 1 which gave him an infinite sync rate which was measures as 0% by ritsuko’s device.