Previous stay in UK counting towards 5 years?

[verity]

Greetings!
I will make this bland for easy reading:

I am a non-EEA national married (but separated) to an EEA national.

September 2006 - September 2008 resided in UK with study visa

September 2008 - June 2009 lived in non-EEA country

August 2009 married EEA national in their home country (EEA)
August 2009 - June 2010 lived in EEA national's home country

June 2010 - present day (June 2013) both EEA national and I have resided in the UK, however, we moved into separate houses in April 2011

Questions:
1. Can my previous 2 years living in the UK count towards the 5 year rule. I suspect not, since there was a 21 month gap in-between

2. Can I apply for ILR in 2015 if I am still married to, but separated from EEA national? or do we need to be divorced in order to apply?

3. Can I apply for ILR if I am divorced from EEA national, but have retained my right of residence?

4. When is the soonest I can begin the application for ILR?

Thank you kindly!

[Nimitta]

September 2006 - September 2008 resided in UK with study visa

September 2008 - June 2009 lived in non-EEA country

August 2009 married EEA national in their home country (EEA)
August 2009 - June 2010 lived in EEA national's home country

June 2010 - present day (June 2013) both EEA national and I have resided in the UK, however, we moved into separate houses in April 2011

Questions:
1. Can my previous 2 years living in the UK count towards the 5 year rule. I suspect not, since there was a 21 month gap in-between

Nope, and not just because of the gap but because you were not a EU family member yet, so you cannot use the EU route for that period.

2. Can I apply for ILR in 2015 if I am still married to, but separated from EEA national? or do we need to be divorced in order to apply?

You might apply for Permanent residence card (no ILR for EU route) in June of 2015 provided your EU spouse have been working/studying etc for 5 years.

3. Can I apply for ILR if I am divorced from EEA national, but have retained my right of residence?

For PR, yes you can. You have to prove that your spouse had been working/studying etc. during the time you were still a married couple + you had been working/studying etc. since divorce.

4. When is the soonest I can begin the application for ILR?

The soonest might be June 2015 provided you meet the requirements I mentioned above. Since you have not mentioned anything about your spouse working/studying etc. there is no way to tell for sure.