1) When you're separated I think you're only eligible for filing under 5 year rule, because 3 year rule requires living in marital union all the time until oath ceremony.
To be eligible under 5 year rule, you needed to spend more than half of time living in the US, e.g. at least 30 months. In addition, you should have not had any trips more than 6 months in these 5 years. If in any of the years you had a trip that was longer than 180 days, then your "clock" for naturalization "resets". You need to start counting time from the day you're back in the US after that long trip.
2) You can always file taxes with $0 return. Getting a return and filing taxes is two different things. Of course, you can write a personal statement explaining how you didn't earn enough to be required to file taxes and attach evidence. But I'd suggest filing those taxes because it's the path of least resistance.