First, I want to thank AcidAgent for his "How to fix gradual loss of sync once and for all" thread.

This thread simplifies the procedure for those who have downloaded 29.75fps sources and found their audio out of sync after encoding.

The software I used to do this were:

TMPGEnc encoder
Super MP3 Editor
Sonic Foundry Sound Forge

Step 1: Run your source thru the TMPGEnc encoder selecting output as ES (video and audio), this will produce your m1v video file and mp2 audio file.

Step 2: Because Sound Forge 7 refused to recognize mp2 files for me, I had to use Super MP3 Editor to convert it into an mp3 file.

Step 3: Use Sound Forge to resample the mp3 at the rate of 44070.

Step 4: While still in Sound Forge trim approximately 3 seconds off your mp3 for every hour of length, then save the mp3.

Step 4: Use TMPGEnc specifying the m1v you created in step 1 as your video source and the resampled mp3 as your audio source.

This should produce a near perfectly synced output mpeg.