EEA Family Permit is not the same as UK spouse visa.
Alan, your wife will not be using form FLR or form ILR.
Your wife will be using residence cards
Your situation doesn't follow 'normal' immigration rules.
EEA nationals and their family members are not granted ILR.
Your wife MAY apply for Permanent Residence (PR) after completing right of residence for five years.
Don't apply before the five year requirement has been met.
The current application form, EEA4, is available for non-EEA national family members who WANT to apply for a Permanent Residence card.
Now, the reason for the highlighted words above for MAY and WANT is simply because your wife already has a route to British Citizenship (Naturalisation).
Family members of a EEA national just have to wait for 6 years, then apply for naturalisation directly (Assuming she did not break residence rules).
A total of six years of residence is required, 5 years to acquire PR and then 1 year as a Permanent Resident.
The Life in the UK Test would be necessary for naturalisation (British Citizenship) but is not required for PR.
ILR is not available for her, that requires leave to remain in an 'appropriate category' of the UK immigration rules.
However permanent residence is also considered as 'settled status'. (same as an ILR holder)