It may be too late now, but given that old of a machine, a couple of suggestions going forward.
1. Transcode all oddball media to ProRes or DNxHD. This would be RED, A7S, DJI, etc.
2. Use the Adobe proxy workflow.
3. Work in a 1080 timeline and then send to Resolve for relinking, color correction, 4K mastering.
4. Upgrade your hardware.
Premiere doesn’t do particularly well above 1080 with mixed codecs and frame rates on these old machines. Newer Premiere versions are improving in that area, but some codecs, like the DJI and A7S are a disaster to work with.
What sort of storage? Your profile says LaCie RAID. Have you run any speed tests? How full? Are you using effects? If so, which ones? Have you tried rendering timeline sections as you go?
Edit: I reread you post and I see you’ve tried some of this. I would not upgrade this old machine to Mojave. I’m not even sure you can without a terminal hack. Sometimes Premiere projects get corrupt. Try copy and pasting your current timeline clips into a new sequence in a fresh, blank project and see if this improves anything. You mentioned proxies. Have you toggled proxies “on” so that you are actually linking to the proxy files and not the originals?
– Oliver
Oliver Peters – oliverpeters.com