Skaven252
I have two .mov video files
Can you share it to me? Public or private. As you wish. If it is not top secret video of-course. 
left camera video.mov - 29,951 fps; length 2:50,680
right camera video.mov - 30,928 fps; length 2:50,655
It is average framerate. You need to know base framerate to convert VFR to CFR without losing of quality and to save original speed.
They are the same length, and play in sync if inserted into a Vegas project
This is good.
They will not pair into a stereoscopic subclip because of too much framerate difference in the media files
I need to look to video.
If I re-encode the files with VirtualDub to just simply force them into the same framerate (29,970), they will drift off sync because of the rate difference
Something wrong with open or with conversion.
Does AviSynth have frame resampling options built in?
Yes. It does, see DirectShowSource(convertfps=true). It converts VFR to CFR.
I also need to apply a fisheye removal to the video
You can process video in avisynth without removing fisheye. I think it will be better to work with source than with Vegas (wrong/buggy) output. It gives better chance to repair drops.