Once you finished the final boss, you can re-load your last save and there are extra bits you need to do in order to get the full pacifist run and second final boss.
The game won't start the events that take you there without first completing the neutral run final boss, even if you did a full pacifist run on your first play through.
I haven't personally tried using the tools in this video, but they may be an easier way to set up virtual machines for specific older hardware/ windows machines for gaming.
https://youtu.be/mWEE2RJj3YI?si=7ToeV7-Zd5d58BYA