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

https://www.videohelp.com/forum/viewtopic.php?t=140540

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.