Take a look at the HMRC helpsheets HS281
which contain relevant information.
A married couple can only have one main residence for Capital Gains Tax purposes between them when they are living together. Separation changes that as you will read on page 3 of HS281.
If the property which you currently let becomes your main home, you will get exemption from CGT for that part of your share of the gain covered by the period that you live in it and for a maximum of the last 18 months of ownership if you are not living in it, excluding overlaps.
As the property will have been both your main home and let, you will also be entitled to a further deduction from the gain called letting relief which will be the lesser of:
2 your share of the gain for the period the property was your main home plus the gain for a maximum of the last 18 months of ownership as described above and
3 that part of the gain covered by the period you let the property less the gain for any part of that period covered by the last 18 months of ownership.
Do, for example, if you live in the property for 3 years and then sell it, you will get main residence relief for 50% of your share of the gain plus letting relief. Any gain left after those deduction will be taxable subject to the annual CGT exemption which is currently £11,000.
For disposals of property which have been the owner's main home at some point which occurred by 5 April 2014, a maximum of the last 36 months of ownership was given as tax free. For disposals after 5 April 2014, it is a maximum of the last 18 months of ownership.
I hope this helps but let me know if you have any further questions.