My advice is going to run counter to all the previous advice posted, but everyone writes differently and there's no telling which of us have a similar creation/thinking method to yours.
I've got three books of PK (one still ongoing but almost finished) out as serials. The first half of Book One sucks, and I'm willing to bet that the first half of everyone's Book One sucks, whether it's a series or a standalone, or a print novel or a serial or what. When you start writing (for the first time or after a years-long hiatus), that first 50,000 words or so is you learning how to walk/swim/ride a bike. It's not all pretty.
However, once you learn how to ride a bike, it's a pretty smooth ride from then on out. You might hit a few bumps or have an unexpected tumble every now and then, but it's occasional, no-big-deal stuff. The thing is, when you post all of your training materials online, they're out for everyone to see. This is the state of PK right now - Book One is a bit of a mess. I get about 300 reads per current (third book) chapter within the first two weeks, though, so I must have been doing something right amidst all the horrors of that learning experience.
What my readers tend to appreciate is that I keep going and they always have something more to read. It's a serial - the big pull is not how perfect the prose is, but what happens next. The pull is the story, the writing comes second. I learn as I go and I take my knocks.
As to a story shifting while you write it... that happens a lot to me. I just pretend I planned it all along. I've had sidestory arcs expand to much longer than I planned them, characters introduce themselves out of the blue and hijack the story to where they wanted it to go, and unexpected pacing elements. For instance, one scene refused to go any farther, and so I ended it before I expected it to end. Then I wrote the scene that wanted to be written, which had different characters and was a country away from the first scene. After that one was done, I was able to go back to the first. Beforehand I would have thought it was a bad idea to split up that first scene with another scene in the middle - after the fact, when I read what I had done, it seemed just right. Shifting a reader elsewhere really does up the tension and keep them on their toes, and the change in pace helped the story from dragging out too much. Subconsciously, I knew this. Consciously, I wanted to do it the boring way. Subconsciously, I am apparently a better writer than I am consciously.
It sounds like your biggest frustration has been in restraining your chapter length. If you have a natural tendency to pace with longer chapters, then write how you naturally write. I know a lot of people say to keep weblit short, but honestly a chapter's gonna grip someone more if it's written in the way it should be. The same goes with stories overall. Maybe the lesson your writing is trying to teach you now is to go with what you feel like writing, not with what logic tells you. So my suggestion is to just write the story from this point on how you feel it should be written, with possibly some transitional chapters to make it flow better. Call the first part Part One, call the second Part Two. Plenty of books are divided into parts. If your format is consistent within each part, then it should be fine. Maybe the introductory part's short chapters will reflect the fact that it is introductory - now that things have gotten started, the story settles into longer chapters.
If your story wants to shift mid-story, I say LET IT - it's your job to make the transition seem on purpose, though. A re-start may be good for you, but it also may be a better idea to finish a story first before rewriting it. I think you'll learn a lot more. Also, in my experience a lot of authors want to scrap everything halfway through a story and just start over. It's a normal part of the writing process, and it's frustrating. I have it happen about three times per book - after the first 30,000, after the first 60,000, and after the first 80-90,000. My books tend to finish up at 110,000 words, so I basically do the "OH NO EVERYTHING SUCKS" flail at quarter intervals. Char's my editor - she's so used to this happening that she starts expecting it at a certain point.
Irk: "Wait, I always do this at right about this stage of a novel, don't I?"
Char: "Yeah, I was waiting for it. "
Neil Gaiman has a similar conversation with his agent for every book that he writes - he forgets it afterwards, every time. And so do I.
Anyway, in conclusion, I really suggest just plowing forward and seeing what you can make of it from this point. Stories do unexpected things, and I find that the more tricks they pull on an author, the more interesting they are to an audience. If you consider yourself the first reader, then it starts to become entertaining. (Except at the 30,000-word intervals. Oh gods.)