The 720p worked great for me in XBMC. I just fired it up in MPC and it's working fine there too. Stuttering issues could be from too slow of a media source, flash drive or? Or a weak PC that isn't capable of keeping up.
Good luck figuring it out, it looks excellent.
I can't wait for a similar release of the first film.
Big thanks to everyone involved in making this project a reality.