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Haven't tried my own fisheye but things to check out:

http://www.andrewhazelden.com/blog/2012 ... ions-pack/
http://www.andrewhazelden.com/blog/2013/08/dome2rect/


You can sideload 180 x 180 material to Milk VR
Add 180x180 to the .mp4 name

https://milkvr.com/#/content/faq

You can get trial versions of AutoPano and Videostitch. I think they can both handle it.

Tech:
http://www.kscottz.com/fish-eye-lens-de ... -stiching/

If you are running a mac you can get this great premiere/FCPX plugin

http://www.dashwood3d.com/360vrtoolbox.php

Has a ton of 360 equirectangular tools

Right now you have to feed the fisheye to sphere plugin 1:1 images, so I nest them in a 1:1 sequence first and line up the edges of the image circle. I suggested to Tim that you can do it in future versions with the effect tab to save the step.

best part of that plugin is you can run the dk2 at the same time and see the effect live.

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I use Batch Builder and Batch Stitcher in PTGui Pro for image sequences for this. It is fast and accurate. PTGui Google groups forum has lots of posts on this.
https://groups.google.com/forum/#!forum/ptgui

Wish Dashwood would port to windows, but the suite heavily leans on the quartz compositor which is OS X only.

I'm not sure if you ever found a way to do this. I searched around and couldn't find anything. I did find a way that worked for me.
I have a Nikon D610 with a 180 degree fisheye lens.
My old technique:
1. Convert the fisheye video into an image sequence
2. Use PTGui to create a 360x180 equirectangular image set.
3. Convert the image sequence back into video.

My new technique:
I manually created a Photoshop 'action' that takes the fisheye lens and converts it into a 360x180 equirectangular image. This action works on every video shot with the same lens.
1. Open the fisheye video in photoshop.
2. Apply the Photoshop action to the video to convert it to 360x180 equirectangular video.
3. Render the video out from photoshop.


Photoshop Action:
To make the action I did the following...

1. I converted a single frame of a fisheye video to a still image.
2. I brought that frame into PTGui and made a 360x180 equirectangular version of it.
3. I took the single frame of fisheye video into photoshop.
4. I took the PTGui 360x180 equirectangular image into photoshop and placed it under the first layer.
5. I set the top fisheye layer to 50% transparent.
5. I scaled (if necessary) the equirectangular layer and positioned it to match directly under the top fisheye layer.
6. Start Recording your action in the actions panel.
7. Use Image>Canvas Size to expand the size of the canvas by about 120% (so that you will have enough room for the transform controls in the next step)
8. Use Edit>Transform>Warp on the top fisheye layer. This took several minutes for me to transform the fisheye layer to match as closely as possible to the equirectangular layer underneath. I was able to get the image to match very closely in all areas except the extreme edges.
9. Use Image>Canvas Size to Expand the size of the canvas to 4096x2048 (or whatever size you want to render your final video out)
10. Stop your recording in the actions panel.

I initially didn't think this would work. But when I tested this on my VR Gear, without extreme scrutiny, I couldn't tell the difference in the video created using the action and the perfect video created using PTGui. If you study the video carefully you will see that the edges are curved a little more in the photoshop actions version of the video. But this is not really noticeable at all. No real distortion anywhere to my eye! Pretty cool!

Autopano Video is fast but expensive and a bit complicated but you can go directly from an mp4 to a rendered frame sequence or mp4 or Cineform avi -- I get about 9 fps on my not very fast PC. I will write an account here of stereo 180 fisheye mp4 conversion with APV shortly. Another fast solution is Touch Designer but I havent tried that.

I am in the same situation. I am recording 4K videos with 2 DSLR Cameras with 180° fisheye lenses and am trying to convert them to equirectangular to play them in the Oculus DK2, but I'm not finding any easy way to do it. 360vrtoolbox would be perfect as I'm a CC user as well but I'm on a PC... so if anyone had another solution, that's be great!

Check out PTGui  You'll have to batch it for video. Hugin is a free still open source stitcher.  All the apps are at least downloadable for testing (watermarkered)

dome2rect + VirtualDub have worked well for me. You still have to convert to images, though.