I gave this a try, but sadly it came up short. For writing a single paper of MSc Thesis, it might work. However it just doesn't seem suited for handling a large number of references for a variety of projects, which get called on frequently as standard references in papers, reference material, and much more.
If it helps I have just under 2000 papers in my Zotero. It isn't massive by research standards, but it is substantial.
Try to group into different projects in F1000. One thing I still don't like about F1000 is the reference manager need to go online for entries, so it kind of slow on first call. By the way, i don't how you cite when writing, but for me, I mostly handle that part after I finish the writing. At the places citations needed in the manuscript, I often just put a mark saying #somebody's paper on somethin#, and then do the job all the once. There always some really prolific guys make the citation search taking too much time to break to flow.
If it helps I have just under 2000 papers in my Zotero. It isn't massive by research standards, but it is substantial.