@ mcarmount
I haven't landed yet but I think I can answer your question.
It would be wise to have the Guidance and Counselling while waiting for the visa if your wife lives close to any of these CFO branches: Manila, Cebu and Davao. Unfortunately you said she lives far from the the first two. How about Davao? Still far?
If so, then just have the Counselling a day or two prior to departure. That would save time and money. There are 2 separate places here in Metro Manila where she can attend: CFO-Taft Avenue in front of De Lassalle University and walking distance from LRT Vito Cruz station; and the other is PRISM-Quezon City.
I'm more familiar with CFO-Taft since I had done mine there and I live close to that place. Your wife can just go there any day (Monday to Friday)8am to 2:30pm. I went there at 10:40am, had the forms filled out and submitted my requirements(photocopy of the following:marriage certificate, birth certificate, Government issued I'd). But was asked to go back at 1pm since I was late at the 10:30am batch.If you want to have it early, then tell her to go at 8am.
PRISM-Quezon City is the one who has the every Tuesday and Friday only schedule.
So I think, it would be more flexible and convenient to go at CFO Taft. Aside from that, it's only 20minutes from the airport.