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premiere has a long history of, and reputation for, falling apart on long timelines. there were several bugs supposedly fixed to help with this and prevent project file corruption, but perhaps they still haven't fixed everything. there is also the possibility of third part plugins somehow contributing to this. its often recommended to have more ram as the project length increases, so going to 64gb might help a little, but i doubt it would make a major difference. if you have the premiere project file and cache on the 3tb hdd, you might copy the project file to the os ssd and set the cache to the ssd too, to see if that helps.
beyond those things, the usual workaround is to split the edit into multiple projects, around 10-20 min long or small enough to keep the amount of imported media small for each project, and then combine each small project together to make the full edit. premiere can import other timelines from other projects, so combining the timelines from each smaller project can be done in a master project that only contains the imported timelines.
Thanks for the input. Unfortunately I don't have enough space on the OS drive to cache the project, might have to resort to breaking the project up as you mentioned, thanks!
its kind of a long shot, but you could still try copying over just the premiere project file. if its a large file it might be faster for premiere to read thru it on the fast ssd. i think the warp stabilizer also makes the project file alot larger as it writes that tracking data to the project file, so doing that stuff last might be better for editing performance.
You could try using "Render and Replace" on the stabilized footage and apply Magic Bullet from there. With the stabilization rendered into the source footage at your Sequence settings, you should be able to get back to a more fluid editing experience.