Hi there RicIre, welcome aboad Filipino UK forum.
As a first step may I kindly suggest you review our forum thread and follow all the included links to the UKBA site.
All New Guide - How to apply for a Spouse/Partner Visa
You should also make searches here in the forum for any areas/topic of concern
I believe you'll be the sponsor of your wife as a British Citizen or Person Settled here.
I'm unsure as to why you're getting concerned about your Naturalisation Certificate. Where does UKBA state it is a documentary requirement?
For the visa application, in terms of ID you (sponsor) will need to supply passport photo-page copy and birth certificate
For getting married in the Philippines I'll reply to your questions in a separate post below.
Please do take some time to review the Application Forms and the UKBA Guide to Supporting Documents.
(Both may be downloaded from this page)
Where does it state this document is required?
Your passport and birth certificate is sufficient as ID for Visa
I've never known anyone have a problem with this. My wife's birth certificate was also very unclear but was not an issue for UKBA.
This is somewhat complicated. My advice is to be sure your UK CNI is exchanged for a local (Philippine) CNI within 3 months. The local CNI is also valid for 3 months.
Technically, the UK CNI has no expiry. However Philippine law requires the document to be used by the Embassy within 3 months, hence the confusion and varying statements.
For interest and completeness I'll post seperately on this below.
The best and most secure option is to follow the protocol of 3 months validity.
No problem
No problem. Very easy. Can also be done online.