Hi There,
1st of all congratulation.
Well i did survey about this because im in same status as you are now... 
OK,
1st your gf must come to malaysia with sosial visit pass, bring her to philippines embassy to apply "Single declaration letter" from Philippines government.. She could do this letter philippines bt it will be in their langguage and u still need to visit Embassy in KL to translate to Malay langguage.
Then once you get the letter u need to visit Ministy of Foreign affair in putrajaya to submit this letter together with application to get permission to marry this girl... once you get approval letter from this department.. you need to visit Marriage registration (IC office) in putrajaya to apply for marriage application. You can choose to have registration marriage there in putrajaya or at your nearest place.. bt if you want to have the registration marriage at your nearest place then u need to get letter from Putrajaya marriage registration office, they will issue a letter that later u need to submit together with registration marriage form at your nearest place...
Once you submit all the documents, they will issue a letter stating u will married with bla..bla bla... so u can use this letter to extend your gf stays in malaysia at Imigresen office... after submittion it will take more then 3 week for actual registration marriage took place.
About PR, according to so called law.. Foreign citizen must stay in Malaysia atleast 5 year to apply for PR...
I hope i answered your questions
