Have you considered using PR (PAL) ex either DRW, MEL or SYD? Better service than QF.
Sometimes ex SYD they use the Boeing 777-300ER, all of which are less than four years old (they now have six, but two are required for the MNL - LHR route) but the ex MEL flights are typically A330s ( a recent appearance, but old planes) or A343s.
I suggest using VA to connect and trying to link the two separately purchased PNRs.
They fly ex MEL on Wed, Fri, Sun and ex SYD on the four other days. The flights ex MNL are overnight on the 'previous' night i.e. Tue, Thu and Sat nights ex MNL for MEL; to SYD on the other nights.
Or you could fly to DRW with VA or QF and connect to PR's three days a week flight (that originates in BNE) mid-afternoon ex DRW. This is always an A320. The online fares ex DRW can be quite cheap.
A good travel agent for PR is North Suburban Travel in Brunswick, Melbourne - 03 9384 1844. You will need to overnight in MNL before flying to MPH as latter does not accommodate night flights.