I suspect you probably know the answer yourself already, but there’s no short cut to hard graft. As a fan of prog and tech metal, the bass parts can be like the guitar parts you’ve described. It’s just a case of breaking up the piece bit by bit, even bar by bar. The very first ‘tricky’ (or what I thought was tricky at the time) bass line was a track called Metropolis Pt2 by some cheeky little prog band. I nearly threw the dodgy transcriptions out the window they were so bad. It took me ages!
These days, I will use my DAW software or the likes of Guitar Pro to loop up sections of the song so I can practice them over and over with a virtual band. The loops will start with bars, then sections. Oh and most importantly.... slowly! Guitar Pro for example allows me to pull the tempo back to ensure proper technique in fast passages as well as remaining relaxed instead of tensing up when the tempo goes past 160 in 16ths or whatever.
keep looping. You are moving sections of music from your short term memory to long term and I understand that from a psychological angle, repetitive well spent practice will enable this better than just staring at the page hoping it will go in.