The wonders of gender-neutral pronouns!

Clock is beginning to take shape, although I am certainly finding it a lot harder to write than either The Binary Man or Heal The Sick, Raise The Dead.  There is not only the challenge of writing my first 100% science fiction book (The Binary Man had only some elements of the future tech, which always took a back seat to the other themes), but also I am finding out how writing something that is intentionally strange and otherworldly can at the same time may be alienating to the reader.  I'm trying to tread a tightrope between the fantastic and the mundane, to cement it as strongly as I can in known physics whilst still retaining it's oddness.  Yet the issue that is bothering me the most at the moment is what to do with my damn pronouns!
Gender is irrelevant in Clock, it doesn't even exist, but after using the term "it" to refer to my protagonist and everyone they meet about a hundred times(which is pretty much the only none gender specific pronoun in the English language), it seems to flood the page and dilute the story.  "It" has so many uses that I'm struggling to keep the narration focused.  The only other option seems to be an invented pronoun.  I was toying with the idea of (S)he, but there is only the cumbersome possessive pronouns attached "her/his" and don't even get me started on "herself/himself"! 
I could alternate between himself and herself, but I want to reduce confusion, not increase it.
There are a lot of invented pronouns that I could use, but none that any apart from linguists are likely to recognise, including "E, Ey, Hu, Per"... they're all on wikipedia, take a look!
It looks like I'm going to have to do a bit of experimenting... and I'm only 2000 words in.  This one will be a quest and a half!