Concerning the passport issue, most folks would suggest to secure early. Minimise risks.
It makes no impact on either visa application or CFO.
The passport can be changed at the Philippine Embassy in London without any problems. Usually the process takes 4 - 5 weeks as it needs to get done in Manila.
Nice day out in London for the wife

From your posting it appears you are heading for a 'Standard' UK entry Visa leading to settlement (Fiancee), but you've got me confused with your mentioning of EEA Family Permit.
Where does an EEA Family Permit fit into your plan? Are you planning to live in EU for a while? The requirements are quite different.