97Mb project file? There’s your problem. I’ve now edited several feature-length docs on FCP, also using PhotoJPEG in the initial rough cut stages. Basically if a project file gets above 10-12Mb (easily achieved on docs with multiple versions), FCP can get flaky, so you need to slim things down and adopt a different workflow.
Break the original project down into separate projects ie. Media/Edits, then further down as necessary into chapters/acts/interviews, whatever seems most logical. Also weed out redundant edits by archiving them, keeping the project with your main edit up to date and as lean as possible.
There’s no problem for FCP to have multiple projects open simultaneously, you can copy, cut and paste between them.
Also, make sure that you regularly save your projects using the “Save As…” dialogue, forcing the whole file to be re-written from the ground up on a regular basis. Apparently months of saving to the same file is a recipe for corruption, and simply backing up a buggy file is no insurance against losing your work.