That's fine. Splitting it is probably smart. I wasn't quite as skilled as i am now, so figuring out how merging and splitting worked was definitely a new endeavor. Probably when i add the tweak (there's an epilogue chapter to put in one story) i can split one or two stories that were technically too large (at least file-wise, they want up to 200k per file, since these should be readable on a phone/tablet and it might only give say 10Mb for viewing, i can understand that).
Worse case you can make the PDF, then use the PdfGear and separate it to say ~500 page blocks (just figure out what page ends the last story you wanted to keep)
Or you can extract the stories/html and make a new book (or deleted unwanted stories), regenerate the TOC and then convert to PDF afterwards... whatever floats your boat.
Though could easily just do story-per-epub/pdf, though that's what they were to start.
I don't recommend PDF, mostly lack of ability to edit, can't replace/optimize images easily, and it's intended for print so zooming in doesn't word-wrap/adjust to fit the screen; Plus it compresses worse. (To my understanding it's a proprietary subset of GhostScript which is a language for printers...)