Sounds like you are on a reasonable track, but you may also want to do a rigid registration first so you at least have the anatomy lined up before cropping and resampling.
But also, check out the lung segmentation tools (GitHub - Slicer/SlicerLungCTAnalyzer: This is a 3D Slicer extension for segmentation and spatial reconstruction of infiltrated, collapsed, and emphysematous areas in lung CT. and New extension: MONAI Auto3DSeg - raise the bar in AI medical image segmentation for example) before investing too much time in new tools.
If there things missing from existing tools please report back here.