DAVE,
Just get your wife to call in at the NSO Local office and ask for secpa, its a shortened form the NSO Marriage Contract issued by them at Quezon City, the paperwork should not take more than 2-3 weeks to be returned, 6 months is ludicrous, and what you can do is use a fixer at QC to obtain it quickly for you, for the usual brown envelope under the table, this amounts to very little normally around P500 or less, but secpa will do the job for the purpose of obtaining a visa at British Embassy, they are well aware of the problems with security paper marriage contracts.
This has been a common problem for visa applicants as far back as I can remember, best of luck.
Pete