Well thanks for you response everyone
Though I had found my own solution after more trials and errors. This was what I did to create my new synced mpeg. All the video/audio techies will probably tell me, your doing it all wrong! but it seems to work fine for me. People you should note, I do not know what I'm doing, I have guessed my way through all of these procedures.
You will need the following:
VirtualDub
MusicMatch 10 (Seems to perfectly convert the VBR to CBR WAV)
Step 01:
Open the file in VirtualDub (plain VirtualDub). Then choose "Audio", "Direct Stream Copy". Then choose "File", "Save WAV". In filename, change .WAV to .MP3, then save it somewhere.
Step 02:
Launch MusicMatch, then choose "File", "Convert Files..",
Check the settings are as follows:
Source Track Type: [mp3],
Convert Selected Tracks to: [wav]
Then point the source frame to the place you saved your file from VirtualDub. Then it will list all the available mp3s it can convert, choose "Start". To let it do so, then it will create a huge WAV file.
PS: Don't get scared by the size of the WAV, this will not normally affect the overall size of the final encoded MPEG.
I hope this works for you as well as it works for me.