Hi Plonker,
It only takes 42 days if you apply for a CNI in the Philippines. If you apply at your local registry office in the UK, it costs about £30 and takes about 23 days. Then when you go to the Philippines, your UK CNI can be exchanged at the British Embassy in Manila or the British Consulate in Cebu while you wait, for the local version which entitles you to marry in the Philippines.
Then, when you have this and the other required documents, you have to apply for a marriage licence, normally, but not neccessarily, where you intend to be married, which usually takes 10 days. While your waiting you can arrange the wedding and go for your pre-marital seminar if it's required in the province where you intend to marry.
With regard to your last point about whether to marry in Phils or the UK, it is of course much cheaper to marry in phils and it's usually a little easier to get a Spouse visa as opposed to a Fiancee visa.
Cheers,
Iain.