Hi - here are a few suggestions for the different categories you mentioned…
PDF Converter, OCR: PDF Pen Pro 2, PDF Studio 2019 (does not look great but works really well)
Citation Manager / PDF storage: Bookends all the way, not sexy but amazing once you learn how to use it properly; Paperpile is great when using Google Docs (+ new iOS app)
Annotation: Highlights + PDF Expert + exploring Liquid Text (now on MacOS)
Knowledge and Note management: Obsidian, Roam Research, DEVONthink Pro, DevonAgent Pro
Final reviews and publication: Mellel works great, now excellent compatibility with Word; amazing if you are using Bookends; have a look at Grammarly and ProWritingAid for final polishing
Adobe suite replacement: The 3 Affinity softwares are top-notch (Design, Photo and Publisher), and no subscription.