I don't see any way to speed this up. I assume that for the first approach you used the "list questions" or "list question groups" feature to delete the undesired questions? I don't see how this could be sped up in any way. It is just choosing the questions you want to delete, tick them and then go for "selected questions..." --> Delete.
Maybe someone else has a good idea.
Off-topic:
Your LimeSurvey version: Version 3.27.9+210726
Your Limesurvey installation is without any updates, bug fixes and security patches since 26/07/2021, so over 1,5 years. You really should consider an update to the latest version of LS3 and for the long run an update to LS5 or LS6, as I assume that LS3 will be EOL rather sooner than later, now that LS6 is out. Currently I would probably still wait a couple of weeks to implement LS6 for production, but an update to the latest LS3 is a good idea for sure.