That is a massively huge world 
, yeah, either Delete, or get the unused scenes into Compendiums (Shared Compendiums are great: How to share content between worlds, especially for things like scene re-use).
The error… I’d take that to the FoundryVTT Discord and the pf2e channel, show them that error on migration. See if they’ve got anything for you. That sure sounds like it hits SOMETHING in your world, and just stops trying to migrate…